Decoding approaches for protein identification

ABSTRACT

Methods and systems are provided for accurate and efficient identification and quantification of proteins. In an aspect, disclosed herein is a method for identifying a protein in a sample of unknown proteins, comprising receiving information of a plurality of empirical measurements performed on the unknown proteins; comparing the information of empirical measurements against a database comprising a plurality of protein sequences, each protein sequence corresponding to a candidate protein among a plurality of candidate proteins; and for each of one or more of the plurality of candidate proteins, generating a probability that the candidate protein generates the information of empirical measurements, a probability that the plurality of empirical measurements is not observed given that the candidate protein is present in the sample, or a probability that the candidate protein is present in the sample; based on the comparison of the information of empirical measurements against the database.

CROSS-REFERENCE

This application is a continuation of U.S. patent application Ser. No.17/221,431, filed Apr. 2, 2021, which is a continuation of U.S. patentapplication Ser. No. 16/534,174, filed Aug. 7, 2019, which is acontinuation of International Application No. PCT/US2018/067985, filedDec. 28, 2018, which claims the benefit of U.S. Provisional PatentApplication No. 62/611,979, filed Dec. 29, 2017; InternationalApplication No. PCT/US2018/067985 is a continuation-in-part ofInternational Application No. PCT/US2018/056807, filed Oct. 20, 2018,each of which is incorporated by reference herein in its entirety.

BACKGROUND

Current techniques for protein identification typically rely upon eitherthe binding and subsequent readout of highly specific and sensitiveaffinity reagents (such as antibodies) or upon peptide-read data(typically on the order of 12-30 amino acids long) from a massspectrometer. Such techniques may be applied to unknown proteins in asample to determine the presence, absence, or quantity of candidateproteins based on analysis of binding measurements of the highlyspecific and sensitive affinity reagents to the protein of interest.

SUMMARY

Recognized herein is a need for improved identification andquantification of proteins within a sample of unknown proteins. Methodsand systems provided herein can significantly reduce or eliminate errorsin identifying proteins in a sample and thereby improve thequantification of said proteins. Such methods and systems may achieveaccurate and efficient identification of candidate proteins within asample of unknown proteins. Such identification may be based oncalculations using information such as binding measurements of affinityreagent probes configured to selectively bind to one or more candidateproteins, protein length, protein hydrophobicity, and isoelectric point.In some embodiments, a sample of unknown proteins may be exposed toindividual affinity reagent probes, pooled affinity reagent probes, or acombination of individual affinity reagent probes and pooled affinityreagent probes. The identification may comprise estimation of aconfidence level that each of one or more candidate proteins is presentin the sample.

Methods and systems provided herein may comprise algorithms foridentifying proteins based on a sequence of experiments performed onfully-intact proteins or protein fragments. Each experiment may be anempirical measurement performed on a protein and may provide informationwhich may be useful for identifying the protein. Examples of experimentsinclude measurement of the binding of an affinity reagent (e.g.,antibody or aptamer), protein length, protein hydrophobicity, andisoelectric point. Information about experimental outcomes may be usedto calculate probabilities or likelihoods of protein candidates and/orto infer protein identity by selecting the protein from a list ofprotein candidates that maximizes the likelihood of the observedexperimental outcomes. Methods and systems provided herein may alsocomprise a collection of protein candidates, and algorithms to calculatethe probability of experimental outcomes from each of these proteincandidates.

In an aspect, the present disclosure provides a computer-implementedmethod for identifying a protein in a sample of unknown proteins, themethod comprising: (a) receiving, by said computer, information of aplurality of empirical measurements performed on said unknown proteinsin said sample; (b) comparing, by said computer, at least a portion ofsaid information of said plurality of said empirical measurementsagainst a database comprising a plurality of protein sequences, eachprotein sequence corresponding to a candidate protein among a pluralityof candidate proteins; and (c) for each of one or more candidateproteins in said plurality of candidate proteins, generating, by saidcomputer, one or more of: (i) a probability that said candidate proteingenerates said information of said plurality of empirical measurements,(ii) a probability that said plurality of empirical measurements is notobserved given that said candidate protein is present in said sample,and (iii) a probability that said candidate protein is present in saidsample; based on said comparison of said at least a portion of saidinformation of said plurality of said empirical measurements againstsaid database comprising said plurality of protein sequences.

In some embodiments, two or more of said plurality of empiricalmeasurements are selected from the group consisting of: (i) bindingmeasurements of each of one or more affinity reagent probes to saidunknown proteins in said sample, each affinity reagent probe configuredto selectively bind to one or more candidate proteins among saidplurality of candidate proteins; (ii) length of one or more of saidunknown proteins in said sample; (iii) hydrophobicity of one or more ofsaid unknown proteins in said sample; and (iv) isoelectric point of oneor more of said unknown proteins in said sample.

In some embodiments, generating said plurality of probabilities furthercomprises receiving additional information of binding measurements ofeach of a plurality of additional affinity reagent probes, eachadditional affinity reagent probe configured to selectively bind to oneor more candidate proteins among said plurality of candidate proteins.In some embodiments, the method further comprises generating, for saideach of one or more candidate proteins, a confidence level that saidcandidate protein matches one of said unknown proteins in said sample.

In some embodiments, said plurality of affinity reagent probes comprisesno more than 50 affinity reagent probes. In some embodiments, saidplurality of affinity reagent probes comprises no more than 100 affinityreagent probes. In some embodiments, said plurality of affinity reagentprobes comprises no more than 200 affinity reagent probes. In someembodiments, said plurality of affinity reagent probes comprises no morethan 300 affinity reagent probes. In some embodiments, said plurality ofaffinity reagent probes comprises no more than 500 affinity reagentprobes. In some embodiments, said plurality of affinity reagent probescomprises more than 500 affinity reagent probes. In some embodiments,the method further comprises generating a paper or electronic reportidentifying said proteins in said sample.

In some embodiments, said sample comprises a biological sample. In someembodiments, said biological sample is obtained from a subject. In someembodiments, the method further comprises identifying a disease state insaid subject based at least on said plurality of probabilities.

In some embodiments, (c) comprises, for each of one or more candidateproteins in said plurality of candidate proteins, generating, by saidcomputer, (i) said probability that said candidate protein generatessaid information of said plurality of empirical measurements. In someembodiments, (c) comprises, for each of one or more candidate proteinsin said plurality of candidate proteins, generating, by said computer,(ii) said probability that said plurality of empirical measurements isnot observed given that said candidate protein is present in saidsample. In some embodiments, (c) comprises, for each of one or morecandidate proteins in said plurality of candidate proteins, generating,by said computer, (iii) said probability that said candidate protein ispresent in said sample. In some embodiments, said measurement outcomecomprises binding of affinity reagent probes. In some embodiments, saidmeasurement outcome comprises non-specific binding of affinity reagentprobes. In some embodiments, said measurement outcome comprises bindingof affinity reagent probes. In some embodiments, said measurementoutcome comprises non-specific binding of affinity reagent probes. Insome embodiments, said empirical measurements comprise binding ofaffinity reagent probes. In some embodiments, said empiricalmeasurements comprise non-specific binding of affinity reagent probes.

In some embodiments, the method further comprises generating asensitivity of protein identification with a pre-determined threshold.In some embodiments, said pre-determined threshold is less than 1% ofbeing incorrect. In some embodiments, said protein in said sample istruncated or degraded. In some embodiments, said protein in said sampledoes not originate from a protein terminus.

In some embodiments, said empirical measurements comprise length of oneor more of said unknown proteins in said sample. In some embodiments,said empirical measurements comprise hydrophobicity of one or more ofsaid unknown proteins in said sample. In some embodiments, saidempirical measurements comprise isoelectric point of one or more of saidunknown proteins in said sample. In some embodiments, said empiricalmeasurements comprise measurements performed on mixtures of antibodies.In some embodiments, said empirical measurements comprise measurementsperformed on samples obtained from a plurality of species. In someembodiments, said empirical measurements comprise measurements performedon samples in the presence of single amino acid variants (SAVs) causedby non-synonymous single-nucleotide polymorphisms (SNPs).

Additional aspects and advantages of the present disclosure will becomereadily apparent to those skilled in this art from the followingdetailed description, wherein only illustrative embodiments of thepresent disclosure are shown and described. As will be realized, thepresent disclosure is capable of other and different embodiments, andits several details are capable of modifications in various obviousrespects, all without departing from the disclosure. Accordingly, thedrawings and description are to be regarded as illustrative in nature,and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.To the extent publications and patents or patent applicationsincorporated by reference contradict the disclosure contained in thespecification, the specification is intended to supersede and/or takeprecedence over any such contradictory material.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings (also “Figure” and “FIG.” herein), of which:

FIG. 1 illustrates an example flowchart of protein identification ofunknown proteins in a biological sample, in accordance with disclosedembodiments.

FIG. 2 illustrates the sensitivity of affinity reagent probes (e.g., thepercent of substrates identified with a false detection rate (FDR) ofless than 1%) plotted against the number of probe recognition sites(e.g., trimer-binding epitopes) in the affinity reagent probe (rangingup to 100 probe recognition sites or trimer-binding epitopes), for threedifferent experimental cases (with 50, 100, and 200 probes used, asdenoted by the gray, black, and white circles, respectively), inaccordance with disclosed embodiments.

FIG. 3 illustrates the sensitivity of affinity reagent probes (e.g., thepercent of substrates identified with a false detection rate (FDR) ofless than 1%) plotted against the number of probe recognition sites(e.g., trimer-binding epitopes) in the affinity reagent probe (rangingup to 700 probe recognition sites or trimer-binding epitopes) for threedifferent experimental cases (with 50, 100, and 200 probes used, asdenoted by the gray, black, and white circles, respectively), inaccordance with disclosed embodiments.

FIG. 4 illustrates plots showing the sensitivity of proteinidentification with experiments using 100 (left), 200 (center), or 300probes (right), in accordance with disclosed embodiments.

FIG. 5 illustrates plots showing the sensitivity of proteinidentification with experiments using various protein fragmentationapproaches. In each of the top row and the bottom row, proteinidentification performance is shown with 50, 100, 200, and 300 affinityreagent measurements (in the 4 panels from left to right), with maximumfragment length values of 50, 100, 200, 300, 400, and 500 (as denoted bythe hexagons, down-pointing triangles, up-pointing triangles, diamonds,rectangles, and circles, respectively), in accordance with disclosedembodiments.

FIG. 6 illustrates plots showing the sensitivity of identification ofhuman proteins (percent of substrates identified at an FDR of less than1%) with experiments using various combinations of types ofmeasurements), in accordance with disclosed embodiments.

FIG. 7 illustrates plots showing the sensitivity of proteinidentification with experiments using 50, 100, 200, or 300 affinityreagent probe passes against unknown proteins from either E. coli,yeast, or human (as denoted by the circles, triangles, and squares,respectively), in accordance with disclosed embodiments.

FIG. 8 illustrates a plot showing the binding probability (y-axis, left)and sensitivity of protein identification (y-axis, right) againstiteration (x-axis), in accordance with disclosed embodiments.

FIG. 9 shows a comparison of the estimated false identification rate tothe true false identification rate for a simulated 200-probe experimentdemonstrates accurate false identification rate estimation, inaccordance with disclosed embodiments.

FIG. 10 illustrates a computer control system that is programmed orotherwise configured to implement methods provided herein.

FIG. 11 illustrates the performance of a censored protein identificationvs. an uncensored protein identification approach.

FIG. 12 illustrates the tolerance of censored protein identification anduncensored protein identification approaches to random “false negative”binding outcomes.

FIG. 13 illustrates the tolerance of censored protein identification anduncensored protein identification approaches to random “false positive”binding outcomes.

FIG. 14 illustrates the performance of censored protein identificationand uncensored protein identification approaches with overestimated orunderestimated affinity reagent binding probabilities.

FIG. 15 illustrates the performance of censored protein identificationand uncensored protein identification approaches using affinity reagentswith unknown binding epitopes.

FIG. 16 illustrates the performance of censored protein identificationand uncensored protein identification approaches using affinity reagentswith missing binding epitopes.

FIG. 17 illustrates the performance of censored protein identificationand uncensored protein identification approaches using affinity reagentstargeting the top 300 most abundant trimers in the proteome, 300randomly selected trimers in the proteome, or the 300 least abundanttrimers in the proteome.

FIG. 18 illustrates the performance of censored protein identificationand uncensored protein identification approaches using affinity reagentswith random or biosimilar off-target sites.

FIG. 19 illustrates the performance of censored protein identificationand uncensored protein identification approaches using a set of optimalaffinity reagents (probes).

FIG. 20 illustrates the performance of censored protein identificationand uncensored protein identification approaches using unmixed candidateaffinity reagents and mixtures of candidate affinity reagents.

FIG. 21 illustrates two hybridization steps in reinforcing a bindingbetween an affinity reagent and a protein, in accordance with someembodiments.

FIG. 22 illustrates the performance of protein identification using acollection of reagents for selective modification and detection of 4amino acids (K, D, C, and W), in accordance with some embodiments.

FIG. 23 illustrates the performance of protein identification using acollection of reagents for selective modification and detection of 20amino acids (R, H, K, D, E, S, T, N, Q, C, G, P, A, V, I, L, M, F, Y,and W), in accordance with some embodiments.

FIG. 24 illustrates the performance of protein identification usingmeasurements of order of amino acids, where all amino acids are measuredwith a detection probability (equal to reaction efficiency) indicated onthe x-axis, and the y-axis indicates the percent of proteins in thesample identified with a false discovery rate below 1%, in accordancewith some embodiments.

DETAILED DESCRIPTION

While various embodiments of the invention have been shown and describedherein, it will be obvious to those skilled in the art that suchembodiments are provided by way of example only. Numerous variations,changes, and substitutions may occur to those skilled in the art withoutdeparting from the invention. It should be understood that variousalternatives to the embodiments of the invention described herein may beemployed.

The term “sample,” as used herein, generally refers to a biologicalsample (e.g., a sample containing protein). The samples may be takenfrom tissue or cells or from the environment of tissue or cells. In someexamples, the sample may comprise, or be derived from, a tissue biopsy,blood, blood plasma, extracellular fluid, dried blood spots, culturedcells, culture media, discarded tissue, plant matter, syntheticproteins, bacterial and/or viral samples, fungal tissue, archaea, orprotozoans. The sample may have been isolated from the source prior tocollection. Samples may comprise forensic evidence. Non-limitingexamples include a fingerprint, saliva, urine, blood, stool, semen, orother bodily fluids isolated from the primary source prior tocollection. In some examples, the protein is isolated from its primarysource (cells, tissue, bodily fluids such as blood, environmentalsamples, etc.) during sample preparation. The sample may be derived froman extinct species including, but not limited to, samples derived fromfossils. The protein may or may not be purified or otherwise enrichedfrom its primary source. In some cases, the primary source ishomogenized prior to further processing. In some cases, cells are lysedusing a buffer such as RIPA buffer. Denaturing buffers may also be usedat this stage. The sample may be filtered or centrifuged to removelipids and particulate matter. The sample may also be purified to removenucleic acids, or may be treated with RNases and DNases. The sample maycontain intact proteins, denatured proteins, protein fragments, orpartially degraded proteins.

The sample may be taken from a subject with a disease or disorder. Thedisease or disorder may be an infectious disease, an immune disorder ordisease, a cancer, a genetic disease, a degenerative disease, alifestyle disease, an injury, a rare disease, or an age related disease.The infectious disease may be caused by bacteria, viruses, fungi, and/orparasites. Non-limiting examples of cancers include Bladder cancer, Lungcancer, Brain cancer, Melanoma, Breast cancer, Non-Hodgkin lymphoma,Cervical cancer, Ovarian cancer, Colorectal cancer, Pancreatic cancer,Esophageal cancer, Prostate cancer, Kidney cancer, Skin cancer,Leukemia, Thyroid cancer, Liver cancer, and Uterine cancer. Someexamples of genetic diseases or disorders include, but are not limitedto, multiple sclerosis (MS), cystic fibrosis, Charcot-Marie-Toothdisease, Huntington's disease, Peutz-Jeghers syndrome, Down syndrome,Rheumatoid arthritis, and Tay-Sachs disease. Non-limiting examples oflifestyle diseases include obesity, diabetes, arteriosclerosis, heartdisease, stroke, hypertension, liver cirrhosis, nephritis, cancer,chronic obstructive pulmonary disease (COPD), hearing problems, andchronic backache. Some examples of injuries include, but are not limitedto, abrasion, brain injuries, bruising, burns, concussions, congestiveheart failure, construction injuries, dislocation, flail chest,fracture, hemothorax, herniated disc, hip pointer, hypothermia,lacerations, pinched nerve, pneumothorax, rib fracture, sciatica, spinalcord injury, tendons ligaments fascia injury, traumatic brain injury,and whiplash. The sample may be taken before and/or after treatment of asubject with a disease or disorder. Samples may be taken before and/orafter a treatment. Samples may be taken during a treatment or atreatment regime. Multiple samples may be taken from a subject tomonitor the effects of the treatment over time. The sample may be takenfrom a subject known or suspected of having an infectious disease forwhich diagnostic antibodies are not available.

The sample may be taken from a subject suspected of having a disease ora disorder. The sample may be taken from a subject experiencingunexplained symptoms, such as fatigue, nausea, weight loss, aches andpains, weakness, or memory loss. The sample may be taken from a subjecthaving explained symptoms. The sample may be taken from a subject atrisk of developing a disease or disorder due to factors such as familialhistory, age, environmental exposure, lifestyle risk factors, orpresence of other known risk factors.

The sample may be taken from an embryo, fetus, or pregnant woman. Insome examples, the sample may comprise of proteins isolated from themother's blood plasma. In some examples, proteins isolated fromcirculating fetal cells in the mother's blood.

The sample may be taken from a healthy individual. In some cases,samples may be taken longitudinally from the same individual. In somecases, samples acquired longitudinally may be analyzed with the goal ofmonitoring individual health and early detection of health issues. Insome embodiments, the sample may be collected at a home setting or at apoint-of-care setting and subsequently transported by a mail delivery,courier delivery, or other transport method prior to analysis. Forexample, a home user may collect a blood spot sample through a fingerprick, which blood spot sample may be dried and subsequently transportedby mail delivery prior to analysis. In some cases, samples acquiredlongitudinally may be used to monitor response to stimuli expected toimpact healthy, athletic performance, or cognitive performance.Non-limiting examples include response to medication, dieting, or anexercise regimen.

Proteins of the sample may be treated to remove modifications that mayinterfere with epitope binding. For example, the protein may beenzymatically treated. For example, the protein may be glycosidasetreated to remove post-translational glycosylation. The protein may betreated with a reducing agent to reduce disulfide binds within theprotein. The protein may be treated with a phosphatase to removephosphate groups. Other non-limiting examples of post-translationalmodifications that may be removed include acetate, amide groups, methylgroups, lipids, ubiquitin, myristoylation, palmitoylation,isoprenylation or prenylation (e.g., farnesol and geranylgeraniol),farnesylation, geranylgeranylation, glypiation, lipoylation, flavinmoiety attachment, phosphopantetheinylation, and retinylidene Schiffbase formation.

Proteins of the sample may be treated by modifying one or more residuesto make them more amenable to being bound by or detected by an affinityreagent. In some cases, proteins of the sample may be treated to retainpost-translational protein modifications that may facilitate or enhanceepitope binding. In some examples, phosphatase inhibitors may be addedto the sample. In some examples, oxidizing agents may be added toprotect disulfide bonds.

Proteins of the sample may be denatured in full or in part. In someembodiments, proteins can be fully denatured. Proteins may be denaturedby application of an external stress such as a detergent, a strong acidor base, a concentrated inorganic salt, an organic solvent (e.g.,alcohol or chloroform), radiation, or heat. Proteins may be denatured byaddition of a denaturing buffer. Proteins may also be precipitated,lyophilized, and suspended in denaturing buffer. Proteins may bedenatured by heating. Methods of denaturing that are unlikely to causechemical modifications to the proteins may be preferred.

Proteins of the sample may be treated to produce shorter polypeptides,either before or after conjugation. Remaining proteins may be partiallydigested with an enzyme such as ProteinaseK to generate fragments or maybe left intact. In further examples the proteins may be exposed toproteases such as trypsin. Additional examples of proteases may includeserine proteases, cysteine proteases, threonine proteases, asparticproteases, glutamic proteases, metalloproteases, and asparagine peptidelyases.

In some cases, it may be useful to remove extremely large and smallproteins (e.g., Titin), e.g., such proteins may be removed by filtrationor other appropriate methods. In some examples, extremely large proteinsmay include proteins that are at least about 400 kilodalton (kD), 450kD, 500 kD, 600 kD, 650 kD, 700 kD, 750 kD, 800 kD, or 850 kD. In someexamples, extremely large proteins may include proteins that are atleast about 8,000 amino acids, about 8,500 amino acids, about 9,000amino acids, about 9,500 amino acids, about 10,000 amino acids, about10,500 amino acids, about 11,000 amino acids, or about 15,000 aminoacids. In some examples, small proteins may include proteins that areless than about 10 kD, 9 kD, 8 kD, 7 kD, 6 kD, 5 kD, 4 kD, 3 kD, 2 kD,or 1 kD. In some examples, small proteins may include proteins that areless than about 50 amino acids, 45 amino acids, 40 amino acids, 35 aminoacids, or about 30 amino acids. Extremely large or small proteins can beremoved by size exclusion chromatography. Extremely large proteins maybe isolated by size exclusion chromatography, treated with proteases toproduce moderately sized polypeptides, and recombined with themoderately size proteins of the sample.

Proteins of the sample may be tagged, e.g., with identifiable tags, toallow for multiplexing of samples. Some non-limiting examples ofidentifiable tags include: fluorophores, fluorescent nanoparticles,quantum dots, magnetic nanoparticles, or DNA barcoded base linkers.Fluorophores used may include fluorescent proteins such as GFP, YFP,RFP, eGFP, mCherry, tdtomato, FITC, Alexa Fluor 350, Alexa Fluor 405,Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 555,Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 647, Alexa Fluor 680,Alexa Fluor 750, Pacific Blue, Coumarin, BODIPY FL, Pacific Green,Oregon Green, Cy3, Cy5, Pacific Orange, TRITC, Texas Red, Phycoerythrin,and Allophcocyanin.

Any number of protein samples may be multiplexed. For example, amultiplexed reaction may contain proteins from 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, about 20, about 25, about 30,about 35, about 40, about 45, about 50, about 55, about 60, about 65,about 70, about 75, about 80, about 85, about 90, about 95, about 100,or more than about 100 initial samples. The identifiable tags mayprovide a way to interrogate each protein as to its sample of origin, ormay direct proteins from different samples to segregate to differentareas or a solid support. In some embodiments, the proteins are thenapplied to a functionalized substrate to chemically attach proteins tothe substrate.

Any number of protein samples may be mixed prior to analysis withouttagging or multiplexing. For example, a multiplexed reaction may containproteins from 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, about 20, about 25, about 30, about 35, about 40, about 45,about 50, about 55, about 60, about 65, about 70, about 75, about 80,about 85, about 90, about 95, about 100, or more than about 100 initialsamples. For example, diagnostics for rare conditions may be performedon pooled samples. Analysis of individual samples may then be performedonly from samples in a pool that tested positive for the diagnostic.Samples may be multiplexed without tagging using a combinatorial poolingdesign in which samples are mixed into pools in a manner that allowssignal from individual samples to be resolved from the analyzed poolsusing computational demultiplexing.

The term “substrate,” as used herein, generally refers to a substratecapable of forming a solid support. Substrates, or solid substrates, canrefer to any solid surface to which proteins can be covalently ornon-covalently attached. Non-limiting examples of solid substratesinclude particles, beads, slides, surfaces of elements of devices,membranes, flow cells, wells, chambers, macrofluidic chambers,microfluidic chambers, channels, microfluidic channels, or any othersurfaces. Substrate surfaces can be flat or curved, or can have othershapes, and can be smooth or textured. Substrate surfaces may containmicrowells. In some embodiments, the substrate can be composed of glass,carbohydrates such as dextrans, plastics such as polystyrene orpolypropylene, polyacrylamide, latex, silicon, metals such as gold, orcellulose, and may be further modified to allow or enhance covalent ornon-covalent attachment of the proteins. For example, the substratesurface may be functionalized by modification with specific functionalgroups, such as maleic or succinic moieties, or derivatized bymodification with a chemically reactive group, such as amino, thiol, oracrylate groups, such as by silanization. Suitable silane reagentsinclude aminopropyltrimethoxysilane, aminopropyltriethoxysilane and4-aminobutyltriethoxysilane. The substrate may be functionalized withN-Hydroxysuccinimide (NETS) functional groups. Glass surfaces can alsobe derivatized with other reactive groups, such as acrylate or epoxy,using, e.g., epoxysilane, acrylatesilane or acrylamidesilane. Thesubstrate and process for protein attachment are preferably stable forrepeated binding, washing, imaging and eluting steps. In some examples,the substrate may be a slide, a flow cell, or a microscaled ornanoscaled structure (e.g., an ordered structure such as microwells,micropillars, single molecule arrays, nanoballs, nanopillars, ornanowires).

The spacing of the functional groups on the substrate may be ordered orrandom. An ordered array of functional groups may be created by, forexample, photolithography, Dip-Pen nanolithography, nanoimprintlithography, nanosphere lithography, nanoball lithography, nanopillararrays, nanowire lithography, scanning probe lithography, thermochemicallithography, thermal scanning probe lithography, local oxidationnanolithography, molecular self-assembly, stencil lithography, orelectron-beam lithography. Functional groups in an ordered array may belocated such that each functional group is less than 200 nanometers(nm), or about 200 nm, about 225 nm, about 250 nm, about 275 nm, about300 nm, about 325 nm, about 350 nm, about 375 nm, about 400 nm, about425 nm, about 450 nm, about 475 nm, about 500 nm, about 525 nm, about550 nm, about 575 nm, about 600 nm, about 625 nm, about 650 nm, about675 nm, about 700 nm, about 725 nm, about 750 nm, about 775 nm, about800 nm, about 825 nm, about 850 nm, about 875 nm, about 900 nm, about925 nm, about 950 nm, about 975 nm, about 1000 nm, about 1025 nm, about1050 nm, about 1075 nm, about 1100 nm, about 1125 nm, about 1150 nm,about 1175 nm, about 1200 nm, about 1225 nm, about 1250 nm, about 1275nm, about 1300 nm, about 1325 nm, about 1350 nm, about 1375 nm, about1400 nm, about 1425 nm, about 1450 nm, about 1475 nm, about 1500 nm,about 1525 nm, about 1550 nm, about 1575 nm, about 1600 nm, about 1625nm, about 1650 nm, about 1675 nm, about 1700 nm, about 1725 nm, about1750 nm, about 1775 nm, about 1800 nm, about 1825 nm, about 1850 nm,about 1875 nm, about 1900 nm, about 1925 nm, about 1950 nm, about 1975nm, about 2000 nm, or more than 2000 nm from any other functional group.Functional groups in a random spacing may be provided at a concentrationsuch that functional groups are on average at least about 50 nm, about100 nm, about 150 nm, about 200 nm, about 250 nm, about 300 nm, about350 nm, about 400 nm, about 450 nm, about 500 nm, about 550 nm, about600 nm, about 650 nm, about 700 nm, about 750 nm, about 800 nm, about850 nm, about 900 nm, about 950 nm, about 1000 nm, or more than 100 nmfrom any other functional group.

The substrate may be indirectly functionalized. For example, thesubstrate may be PEGylated and a functional group may be applied to allor a subset of the PEG molecules. The substrate may be functionalizedusing techniques suitable for microscaled or nanoscaled structures(e.g., an ordered structure such as microwells, micropillars, singlemolecular arrays, nanoballs, nanopillars, or nanowires).

The substrate may comprise any material, including metals, glass,plastics, ceramics or combinations thereof. In some preferredembodiments, the solid substrate can be a flow cell. The flow cell canbe composed of a single layer or multiple layers. For example, a flowcell can comprise a base layer (e.g., of boro silicate glass), a channellayer (e.g., of etched silicon) overlaid upon the base layer, and acover, or top, layer. When the layers are assembled together, enclosedchannels can be formed having inlet/outlets at either end through thecover. The thickness of each layer can vary, but is preferably less thanabout 1700 μm. Layers can be composed of suitable materials such asphotosensitive glasses, borosilicate glass, fused silicate, PDMS, orsilicon. Different layers can be composed of the same material ordifferent materials.

In some embodiments, flow cells can comprise openings for channels onthe bottom of the flow cell. A flow cell can comprise millions ofattached target conjugation sites in locations that can be discretelyvisualized. In some embodiments, various flow cells of use withembodiments of the invention can comprise different numbers of channels(e.g., 1 channel, 2 or more channels, 3 or more channels, 4 or morechannels, 6 or more channels, 8 or more channels, 10 or more channels,12 or more channels, 16 or more channels, or more than 16 channels).Various flow cells can comprise channels of different depths or widths,which may be different between channels within a single flow cell, ordifferent between channels of different flow cells. A single channel canalso vary in depth and/or width. For example, a channel can be less thanabout 50 μm deep, about 50 μm deep, less than about 100 μm deep, about100 μm deep, about 100 μm about 500 μm deep, about 500 μm deep, or morethan about 500 μm deep at one or more points within the channel.Channels can have any cross sectional shape, including but not limitedto a circular, a semi-circular, a rectangular, a trapezoidal, atriangular, or an ovoid cross-section.

The proteins may be spotted, dropped, pipetted, flowed, washed orotherwise applied to the substrate. In the case of a substrate that hasbeen functionalized with a moiety such as an NHS ester, no modificationof the protein is required. In the case of a substrate that has beenfunctionalized with alternate moieties (e.g., a sulfhydryl, amine, orlinker nucleic acid), a crosslinking reagent (e.g., disuccinimidylsuberate, NHS, sulphonamides) may be used. In the case of a substratethat has been functionalized with linker nucleic acid, the proteins ofthe sample may be modified with complementary nucleic acid tags.

Photo-activatable cross linkers may be used to direct cross linking of asample to a specific area on the substrate. Photo-activatable crosslinkers may be used to allow multiplexing of protein samples byattaching each sample in a known region of the substrate.Photo-activatable cross linkers may allow the specific attachment ofproteins which have been successfully tagged, for example, by detectinga fluorescent tag before cross linking a protein. Examples ofphoto-activatable cross linkers include, but are not limited to,N-5-azido-2-nitrobenzoyloxysuccinimide, sulfosuccinimidyl6-(4′-azido-2′-nitrophenylamino)hexanoate, succinimidyl4,4′-azipentanoate, sulfosuccinimidyl 4,4′-azipentanoate, succinimidyl6-(4,4′-azipentanamido)hexanoate, sulfosuccinimidyl6-(4,4′-azipentanamido)hexanoate, succinimidyl2-((4,4′-azipentanamido)ethyl)-1,3′-dithiopropionate, andsulfosuccinimidyl 2((4,4′-azipentanamido)ethyl)-1,3′-dithiopropionate.

The polypeptides may be attached to the substrate by one or moreresidues. In some examples, the polypeptides may be attached via the Nterminal, C terminal, both terminals, or via an internal residue.

In addition to permanent crosslinkers, it may be appropriate for someapplications to use photo-cleavable linkers and that doing so enablesproteins to be selectively extracted from the substrate followinganalysis. In some cases photo-cleavable cross linkers may be used forseveral different multiplexed samples. In some cases photo-cleavablecross linkers may be used from one or more samples within a multiplexedreaction. In some cases a multiplexed reaction may comprise controlsamples cross linked to the substrate via permanent crosslinkers andexperimental samples cross linked to the substrate via photo-cleavablecrosslinkers.

Each conjugated protein may be spatially separated from each otherconjugated protein such that each conjugated protein is opticallyresolvable. Proteins may thus be individually labeled with a uniquespatial address. In some embodiments, this can be accomplished byconjugation using low concentrations of protein and low density ofattachment sites on the substrate so that each protein molecule isspatially separated from each other protein molecule. In examples wherephoto-activatable crosslinkers are used a light pattern may be used suchthat proteins are affixed to predetermined locations.

In some embodiments, each protein may be associated with a uniquespatial address. For example, once the proteins are attached to thesubstrate in spatially separated locations, each protein can be assignedan indexed address, such as by coordinates. In some examples, a grid ofpre-assigned unique spatial addresses may be predetermined. In someembodiments the substrate may contain easily identifiable fixed markssuch that placement of each protein can be determined relative to thefixed marks of the substrate. In some examples, the substrate may havegrid lines and/or and “origin” or other fiducials permanently marked onthe surface. In some examples, the surface of the substrate may bepermanently or semi-permanently marked to provide a reference by whichto locate cross linked proteins. The shape of the patterning itself,such as the exterior border of the conjugated polypeptides, may also beused as fiducials for determining the unique location of each spot.

The substrate may also contain conjugated protein standards andcontrols. Conjugated protein standards and controls may be peptides orproteins of known sequence which have been conjugated in knownlocations. In some examples, conjugated protein standards and controlsmay serve as internal controls in an assay. The proteins may be appliedto the substrate from purified protein stocks, or may be synthesized onthe substrate through a process such as Nucleic Acid-ProgrammableProtein Array (NAPPA).

In some examples, the substrate may comprise fluorescent standards.These fluorescent standards may be used to calibrate the intensity ofthe fluorescent signals from assay to assay. These fluorescent standardsmay also be used to correlate the intensity of a fluorescent signal withthe number of fluorophores present in an area. Fluorescent standards maycomprise some or all of the different types of fluorophores used in theassay.

Once the substrate has been conjugated with the proteins from thesample, multi-affinity reagent measurements can be performed. Themeasurement processes described herein may utilize various affinityreagents. In some embodiments, multiple affinity reagents may be mixedtogether and measurements may be performed on the binding of theaffinity reagent mixture to the protein-substrate conjugate. In somecases, measurements performed on the binding of affinity reagentmixtures may vary across different solvent conditions and/or proteinfolding conditions; therefore, repeated measurements may be performed onthe same affinity reagent or set of affinity reagents, under suchvarying solvent conditions and/or protein folding conditions, in orderto obtain different sets of binding measurements. In some cases,different sets of binding measurements may be obtained by performingrepeated measurements on samples in which proteins have beenenzymatically treated (e.g., with glycosidase, phosphorylase, orphosphatase) or not enzymatically treated.

The term “affinity reagent,” as used herein, generally refers to areagent that binds proteins or peptides with reproducible specificity.For example, the affinity reagents may be antibodies, antibodyfragments, aptamers, mini-protein binders, or peptides. In someembodiments, mini-protein binders may comprise protein binders that maybe between 30-210 amino acids in length. In some embodiments,mini-protein binders may be designed. For example, protein binders mayinclude peptide macrocycles, (e.g., as described in [Hosseinzadeh etal., “Comprehensive computational design of ordered peptidemacrocycles,” Science, 2017 Dec. 15; 358(6369): 1461-1466], which isincorporated herein by reference in its entirety). In some embodiments,monoclonal antibodies may be preferred. In some embodiments, antibodyfragments such as Fab fragments may be preferred. In some embodiments,the affinity reagents may be commercially available affinity reagents,such as commercially available antibodies. In some embodiments, thedesired affinity reagents may be selected by screening commerciallyavailable affinity reagents to identify those with usefulcharacteristics.

The affinity reagents may have high, moderate, or low specificity. Insome examples, the affinity reagents may recognize several differentepitopes. In some examples, the affinity reagents may recognize epitopespresent in two or more different proteins. In some examples, theaffinity reagents may recognize epitopes present in many differentproteins. In some cases, an affinity reagent used in the methods of thisdisclosure may be highly specific for a single epitope. In some cases,an affinity reagent used in the methods of this disclosure may be highlyspecific for a single epitope containing a post-translationalmodification. In some cases, affinity reagents may have highly similarepitope specificity. In some cases, affinity reagents with highlysimilar epitope specificity may be designed specifically to resolvehighly similar protein candidate sequences (e.g. candidates with singleamino acid variants or isoforms). In some cases, affinity reagents mayhave highly diverse epitope specificity to maximize protein sequencecoverage. In some embodiments, experiments may be performed in replicatewith the same affinity probe with the expectation that the results maydiffer, and thus provide additional information for proteinidentification, due to the stochastic nature of probe binding to theprotein-substrate.

In some cases, the specific epitope or epitopes recognized by anaffinity reagent may not be fully known. For example, affinity reagentsmay be designed or selected for binding specifically to one or morewhole proteins, protein complexes, or protein fragments withoutknowledge of a specific binding epitope. Through a qualificationprocess, the binding profile of this reagent may have been elaborated.Even though the specific binding epitope(s) are unknown, bindingmeasurements using said affinity reagent may be used to determineprotein identity. For example, a commercially-available antibody oraptamer designed for binding to a protein target may be used as anaffinity reagent. Following qualification under assay conditions (e.g.,fully folded, partially denaturing, or fully denaturing), binding ofthis affinity reagent to an unknown protein may provide informationabout the identity of the unknown protein. In some cases, a collectionof protein-specific affinity reagents (e.g., commercially-availableantibodies or aptamers) may be used to generate protein identifications,either with or without knowledge of the specific epitopes they target.In some cases, the collection of protein-specific affinity reagents maycomprise about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000,2000, 3000, 4000, 5000, 10000, 20000, or more than 20000 affinityreagents. In some cases, the collection of affinity reagents maycomprise all commercially-available affinity reagents demonstratingtarget-reactivity in a specific organism. For example, a collection ofprotein-specific affinity reagents may be assayed in series, withbinding measurements for each affinity reagent made individually. Insome cases, subsets of the protein-specific affinity reagents may bemixed prior to binding measurement. For example, for each bindingmeasurement pass, a new mixture of affinity reagents may be selectedcomprising a subset of the affinity reagents selected at random from thecomplete set. For example, each subsequent mixture may be generated inthe same random manner, with the expectation that many of the affinityreagents will be present in more than one of the mixtures. In somecases, protein identifications may be generated more rapidly usingmixtures of protein-specific affinity reagents. In some cases, suchmixtures of protein-specific affinity reagents may increase thepercentage of unknown proteins for which an affinity reagent binds inany individual pass. Mixtures of affinity reagents may comprise about1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more than 90% ofall available affinity reagents. Mixtures of affinity reagents assessedin a single experiment may or may not share individual affinity reagentsin common. In some cases, there may be multiple different affinityreagents within a collection that bind to the same protein. In somecases, each affinity reagent in the collection may bind to a differentprotein. In cases where multiple affinity reagents with affinity for thesame protein bind to a single unknown protein, confidence in theidentity of the unknown protein being the common target of said affinityreagents may increase. In some cases, using multiple protein affinityreagents targeting the same protein may provide redundancy in caseswhere the multiple affinity reagents bind different epitopes on the sameprotein, and binding of only a subset of the affinity reagents targetingthat protein may be interfered with by post-translational modificationsor other steric hinderance of a binding epitope. In some cases, bindingof affinity reagents for which the binding epitope is unknown may beused in conjunction with binding measurements of affinity reagents forwhich the binding epitope is known to generate protein identifications.

In some examples, one or more affinity reagents may be chosen to bindamino acid motifs of a given length, such as 2, 3, 4, 5, 6, 7, 8, 9, 10,or more than 10 amino acids. In some examples, one or more affinityreagents may be chosen to bind amino acid motifs of a range of differentlengths from 2 amino acids to 40 amino acids.

In some cases, the affinity reagents may be labeled with nucleic acidbarcodes. In some examples, nucleic acid barcodes may be used to purifyaffinity reagents after use. In some examples, nucleic acid barcodes maybe used to sort the affinity reagents for repeated uses. In some cases,the affinity reagents may be labeled with fluorophores which may be usedto sort the affinity reagents after use.

The family of affinity reagents may comprise one or more types ofaffinity reagents. For example, the methods of the present disclosuremay use a family of affinity reagents comprising one or more ofantibodies, antibody fragments, Fab fragments, aptamers, peptides, andproteins.

The affinity reagents may be modified. Examples of modificationsinclude, but are not limited to, attachment of a detection moiety.Detection moieties may be directly or indirectly attached. For example,the detection moiety may be directly covalently attached to the affinityreagent, or may be attached through a linker, or may be attached throughan affinity reaction such as complementary nucleic acid tags or a biotinstreptavidin pair. Attachment methods that are able to withstand gentlewashing and elution of the affinity reagent may be preferred.

Affinity reagents may be tagged, e.g., with identifiable tags, to allowfor identification or quantification of binding events (e.g., withfluorescence detection of binding events). Some non-limiting examples ofidentifiable tags include: fluorophores, magnetic nanoparticles, ornucleic acid barcoded base linkers. Fluorophores used may includefluorescent proteins such as GFP, YFP, RFP, eGFP, mCherry, tdtomato,FITC, Alexa Fluor 350, Alexa Fluor 405, Alexa Fluor 488, Alexa Fluor532, Alexa Fluor 546, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594,Alexa Fluor 647, Alexa Fluor 680, Alexa Fluor 750, Pacific Blue,Coumarin, BODIPY FL, Pacific Green, Oregon Green, Cy3, Cy5, PacificOrange, TRITC, Texas Red, Phycoerythrin, and Allophcocyanin.Alternatively, affinity reagents may be untagged, such as when bindingevents are directly detected, e.g., with surface plasmon resonance (SPR)detection of binding events.

Examples of detection moieties include, but are not limited to,fluorophores, bioluminescent proteins, nucleic acid segments including aconstant region and barcode region, or chemical tethers for linking to ananoparticle such as a magnetic particle. For example, affinity reagentsmay be tagged with DNA barcodes, which can then be explicitly sequencedat their locations. As another example, sets of different fluorophoresmay be used as detection moieties by fluorescence resonance energytransfer (FRET) detection methods. Detection moieties may includeseveral different fluorophores with different patterns of excitation oremission.

The detection moiety may be cleavable from the affinity reagent. Thiscan allow for a step in which the detection moieties are removed fromaffinity reagents that are no longer of interest to reduce signalcontamination.

In some cases, the affinity reagents are unmodified. For example, if theaffinity reagent is an antibody then the presence of the antibody may bedetected by atomic force microscopy. The affinity reagents may beunmodified and may be detected, for example, by having antibodiesspecific to one or more of the affinity reagents. For example, if theaffinity reagent is a mouse antibody, then the mouse antibody may bedetected by using an anti-mouse secondary antibody. Alternatively, theaffinity reagent may be an aptamer which is detected by an antibodyspecific for the aptamer. The secondary antibody may be modified with adetection moiety as described above. In some cases, the presence of thesecondary antibody may be detected by atomic force microscopy.

In some examples, the affinity reagents may comprise the samemodification, for example, a conjugated green fluorescent protein, ormay comprise two or more different types of modification. For example,each affinity reagent may be conjugated to one of several differentfluorescent moieties, each with a different wavelength of excitation oremission. This may allow multiplexing of the affinity reagents asseveral different affinity reagents may be combined and/ordistinguished. In one example, a first affinity reagent may beconjugated to a green fluorescent protein, a second affinity reagent maybe conjugated to a yellow fluorescent protein and a third affinityreagent may be conjugated to a red fluorescent protein, thus the threeaffinity reagents can be multiplexed and identified by theirfluorescence. In a further example a first, fourth, and seventh affinityreagent may be conjugated to a green fluorescent protein, a second,fifth, and eighth affinity reagent may be conjugated to a yellowfluorescent protein, and a third, sixth, and ninth affinity reagent maybe conjugated to a red fluorescent protein; in this case, the first,second, and third affinity reagents may be multiplexed together whilethe second, fourth, and seventh affinity reagents and the third, sixth,and ninth affinity reagents form two further multiplexing reactions. Thenumber of affinity reagents which can be multiplexed together may dependon the detection moieties used to differentiate them. For example, themultiplexing of affinity reagents labeled with fluorophores may belimited by the number of unique fluorophores available. For furtherexample, the multiplexing of affinity reagents labeled with nucleic acidtags may be determined by the length of the nucleic acid bar code.Nucleic acids may be deoxyribonucleic acid (DNA) or ribonucleic acid(RNA).

The specificity of each affinity reagent can be determined prior to usein an assay. The binding specificity of the affinity reagents can bedetermined in a control experiment using known proteins. Any appropriateexperimental methods may be used to determine the specificity of theaffinity reagent. In one example, a substrate may be loaded with knownprotein standards at known locations and used to assess the specificityof a plurality of affinity reagents. In another example, a substrate maycontain both experimental samples and a panel of controls and standards,such that the specificity of each affinity reagent can be calculatedfrom the binding to the controls and standards and then used to identifythe experimental samples. In some cases, affinity reagents with unknownspecificity may be included along with affinity reagents of knownspecificity, data from the known specificity affinity reagents may beused to identify proteins, and the pattern of binding of the unknownspecificity affinity reagents to the identified proteins may be used todetermine their binding specificity. It is also possible to reconfirmthe specificity of any individual affinity reagent by using the knownbinding data of other affinity reagents to assess which proteins theindividual affinity reagent bound. In some cases, the frequency ofbinding of the affinity reagent to each known protein conjugated to thesubstrate may be used to derive a probability of binding to any of theproteins on the substrate. In some cases, the frequency of binding toknown proteins containing an epitope (e.g., an amino acid sequence orpost-translational modification) may be used to determine theprobability of binding of the affinity reagent to a particular epitope.Thus with multiple uses of an affinity reagent panel, the specificitiesof the affinity reagents may be increasingly refined with eachiteration. While affinity reagents that are uniquely specific toparticular proteins may be used, methods described herein may notrequire them. Additionally, methods may be effective on a range ofspecificities. In some examples, methods described herein may beparticularly efficient when affinity reagents are not specific to anyparticular protein, but are instead specific to amino acid motifs (e.g.,the tri-peptide AAA).

In some examples, the affinity reagents may be chosen to have high,moderate, or low binding affinities. In some cases, affinity reagentswith low or moderate binding affinities may be preferred. In some cases,the affinity reagents may have dissociation constants of about 10⁻³ M,10⁻⁴ M, 10⁻⁵ M, 10⁻⁶ M, 10⁻⁷ M, 10⁻⁸ M, 10⁻⁹ M, 10⁻¹⁰ M, or less thanabout 10⁻¹⁰M. In some cases the affinity reagents may have dissociationconstants of greater than about 10⁻¹⁰M, 10⁻⁹ M, 10⁻⁸ M, 10⁻⁷ M, 10⁻⁶ M,10⁻⁵ M, 10⁻⁴ M, 10⁻³ M, 10⁻² M, or greater than 10⁻² M. In some cases,affinity reagents with low or moderate k_(off) rates or moderate or highk_(on) rates may be preferred.

Some of the affinity reagents may be chosen to bind modified amino acidsequences, such as phosphorylated or ubiquitinated amino acid sequences.In some examples, one or more affinity reagents may be chosen to bebroadly specific for a family of epitopes that may be contained by oneor more proteins. In some examples, one or more affinity reagents maybind two or more different proteins. In some examples, one or moreaffinity reagents may bind weakly to their target or targets. Forexample, affinity reagents may bind less than 10%, less than 10%, lessthan 15%, less than 20%, less than 25%, less than 30%, or less than 35%to their target or targets. In some examples, one or more affinityreagents may bind moderately or strongly to their target or targets. Forexample, affinity reagents may bind more than 35%, more than 40%, morethan 45%, more than 60%, more than 65%, more than 70%, more than 75%,more than 80%, more than 85%, more than 90%, more than 91%, more than92%, more than 93%, more than 94%, more than 95%, more than 96%, morethan 97%, more than 98%, or more than 99% to their target or targets.

To compensate for weak binding, an excess of the affinity reagent may beapplied to the substrate. The affinity reagent may be applied at about a1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, or 10:1 excess relative tothe sample proteins. The affinity reagent may be applied at about a 1:1,2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, or 10:1 excess relative to theexpected incidence of the epitope in the sample proteins.

To compensate for high affinity reagent dissociation rates, a linkermoiety may be attached to each affinity reagent and used to reversiblylink bound affinity reagents to the substrate or unknown protein towhich it binds. For example, a DNA tag may be attached to the end ofeach affinity reagent and a different DNA tag attached to the substrateor each unknown protein. After the affinity reagent is hybridized withthe unknown proteins, a linker DNA complementary to the affinityreagent-associated DNA tag on one end and the substrate-associated tagon the other may be washed over the chip to bind the affinity reagent tothe substrate and prevent the affinity reagent from dissociating priorto measurement. After binding, the linked affinity reagent may bereleased by washing in the presence of heat or high salt concentrationto disrupt the DNA linker bond.

FIG. 21 illustrates two hybridization steps in reinforcing a bindingbetween an affinity reagent and a protein, in accordance with someembodiments. In particular, step 1 of FIG. 21 illustrates an affinityreagent hybridization. As seen in step 1, affinity reagent 2110hybridizes to protein 2130. Protein 2130 is bound to a slide 2105. Asseen in step 1, affinity reagent 2110 has a DNA tag 2120 attached. Insome embodiments, an affinity reagent may have more than one DNA tagattached. In some embodiments, an affinity reagent may have 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more than20 DNA tags attached. DNA tag 2120 comprises a single-stranded DNA(ssDNA) tag having a recognition sequence 2125. Additionally, protein2130 comprises two DNA tags 2140. In some embodiments, DNA tags may beadded using chemistry that reacts with cysteines in a protein. In someembodiments, a protein may have more than one DNA tag attached. In someembodiments, a protein may have 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70,75, 80, 85, 90, 95, 100, or more than 100 DNA tags attached. Each DNAtag 2140 comprises an ssDNA tag having a recognition sequence 2145.

As seen in step 2, DNA linker 2150 hybridizes to DNA tags 2120 and 2140attached to affinity reagent 2110 and protein 2130, respectively. DNAlinker 2150 comprises ssDNA having complementary sequences torecognition sequences 2125 and 2145, respectively. Further, recognitionsequences 2125 and 2145 are situated on DNA linker 2150 so as to allowfor DNA linker 2150 to bind to both DNA tags 2120 and 2140 at the sametime, as illustrated in step 2. In particular, a first region 2152 ofDNA linker 2150 selectively hybridizes to recognition sequence 2125, anda second region 2154 of DNA linker 2150 selectively hybridizes torecognition sequence 2145. In some embodiments, first region 2152 andsecond region 2154 may be spaced apart from each other on the DNAlinker. In particular, in some embodiments, a first region of a DNAlinker and a second region of a DNA linker may be spaced apart with anon-hybridizing spacer sequence between the first region and the secondregion. Further, in some embodiments, a sequence of recognition sequencemay be less than fully complementary to a DNA linker and may still bindto the DNA linker sequence. In some embodiments, a length of arecognition sequence may be less than 5 nucleotides, 5 nucleotides, 6nucleotides, 7 nucleotides, 8 nucleotides, 9 nucleotides, 10nucleotides, 11 nucleotides, 12 nucleotides, 13 nucleotides, 14nucleotides, 15 nucleotides, 16 nucleotides, 17 nucleotides, 18nucleotides, 19 nucleotides, 20 nucleotides, 21 nucleotides, 22nucleotides, 23 nucleotides, 24 nucleotides, 25 nucleotides, 26nucleotides, 27 nucleotides, 28 nucleotides, 29 nucleotides, or 30nucleotides, or more than 30 nucleotides. In some embodiments, arecognition sequence may have one or more mismatches to a complementaryDNA tag sequence. In some embodiments, approximately 1 in 10 nucleotidesof a recognition sequence may be mismatched with a complementary DNA tagsequence and may still hybridize with the complementary DNA tagsequence. In some embodiments, less than 1 in 10 nucleotides of arecognition sequence may be mismatched with a complementary DNA tagsequence and may still hybridize with the complementary DNA tagsequence. In some embodiments, approximately 2 in 10 nucleotides of arecognition sequence may be mismatched with a complementary DNA tagsequence and may still hybridize with the complementary DNA tagsequence. In some embodiments, more than 2 in 10 nucleotides of arecognition sequence may be mismatched with a complementary DNA tagsequence and may still hybridize with the complementary DNA tagsequence.

The affinity reagents may also comprise a magnetic component. Themagnetic component may be useful for manipulating some or all boundaffinity reagents into the same imaging plane or z stack. Manipulatingsome or all affinity reagents into the same imaging plane may improvethe quality of the imaging data and reduce noise in the system.

The term “detector,” as used herein, generally refers to a device thatis capable of detecting a signal, including a signal indicative of thepresence or absence of a binding event of an affinity reagent to aprotein. The signal may be a direct signal indicative of the presence orabsence of a binding event, such as a surface plasmon resonance (SPR)signal. The signal may be an indirect signal indicative of the presenceor absence of a binding event, such as a fluorescent signal. In somecases, a detector can include optical and/or electronic components thatcan detect signals. The term “detector” may be used in detectionmethods. Non-limiting examples of detection methods include opticaldetection, spectroscopic detection, electrostatic detection,electrochemical detection, magnetic detection, fluorescence detection,surface plasmon resonance (SPR), and the like. Examples of opticaldetection methods include, but are not limited to, fluorimetry andUV-vis light absorbance. Examples of spectroscopic detection methodsinclude, but are not limited to, mass spectrometry, nuclear magneticresonance (NMR) spectroscopy, and infrared spectroscopy. Examples ofelectrostatic detection methods include, but are not limited to, gelbased techniques, such as, gel electrophoresis. Examples ofelectrochemical detection methods include, but are not limited to,electrochemical detection of amplified product after high-performanceliquid chromatography separation of the amplified products.

Protein Identification in a Sample

Proteins are vital building blocks of cells and tissues of livingorganisms. A given organism produces a large set of different proteins,typically referred to as the proteome. The proteome may vary with timeand as a function of various stages (e.g., cell cycle stages or diseasestates) that a cell or organism undergoes. A large-scale study ormeasurement (e.g., experimental analysis) of proteomes may be referredto as proteomics. In proteomics, multiple methods exist to identifyproteins, including immunoassays (e.g., enzyme-linked immunosorbentassay (ELISA) and Western blot), mass spectroscopy-based methods (e.g.,matrix-assisted laser desorption/ionization (MALDI) and electrosprayionization (ESI)), hybrid methods (e.g., mass spectrometric immunoassay(MSIA)), and protein microarrays. For example, single-moleculeproteomics methods may attempt to infer the identity of proteinmolecules in a sample by diverse approaches, ranging from directfunctionalization of amino acids to using affinity reagents. Theinformation or measurements gathered from such approaches are typicallyanalyzed by suitable algorithms to identify the proteins present in thesample.

Accurate quantification of proteins may also encounter challenges owingto lack of sensitivity, lack of specificity, and detector noise. Inparticular, accurate quantification of proteins in a sample mayencounter challenges owing to random and unpredictable systematicvariations in signal level of detectors, which can cause errors inidentifying and quantifying proteins. In some cases, instrument anddetection systematics can be calibrated and removed by monitoringinstrument diagnostics and common-mode behavior. However, binding ofproteins (e.g., by affinity reagent probes) is inherently aprobabilistic process which may have less than ideal sensitivity andspecificity of binding.

The present disclosure provides methods and systems for accurate andefficient identification of proteins. Methods and systems providedherein can significantly reduce or eliminate errors in identifyingproteins in a sample. Such methods and systems may achieve accurate andefficient identification of candidate proteins within a sample ofunknown proteins. The protein identification may be based oncalculations using information of empirical measurements of the unknownproteins in the sample. For example, empirical measurements may includebinding information of affinity reagent probes which are configured toselectively bind to one or more candidate proteins, protein length,protein hydrophobicity, and/or isoelectric point. The proteinidentification may be optimized to be computable within a minimal memoryfootprint. The protein identification may comprise estimation of aconfidence level that each of one or more candidate proteins is presentin the sample.

In an aspect, disclosed herein is a computer-implemented method 100 foridentifying a protein within a sample of unknown proteins (e.g., asillustrated in FIG. 1). The method may be applied independently to eachunknown protein in the sample, to generate a collection of proteinsidentified in the sample. Protein quantities may be calculated bycounting the number of identifications for each candidate protein. Themethod for identifying a protein may comprise receiving, by thecomputer, information of a plurality of empirical measurements of theunknown protein in the sample (e.g., step 105). The empiricalmeasurements may comprise (i) binding measurements of each of one ormore affinity reagent probes to one or more of the unknown proteins inthe sample, (ii) length of one or more of the unknown proteins; (iii)hydrophobicity of one or more of the unknown proteins; and/or (iv)isoelectric point of one or more of the unknown proteins. In someembodiments, a plurality of affinity reagent probes may comprise a poolof a plurality of individual affinity reagent probes. For example, apool of affinity reagent probes may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10,or more than 10 types of affinity reagent probes. In some embodiments, apool of affinity reagent probes may comprise 2 types of affinity reagentprobes that combined make up a majority of the composition of theaffinity reagent probes in the pool of affinity reagent probes. In someembodiments, a pool of affinity reagent probes may comprise 3 types ofaffinity reagent probes that combined make up a majority of thecomposition of the affinity reagent probes in the pool of affinityreagent probes. In some embodiments, a pool of affinity reagent probesmay comprise 4 types of affinity reagent probes that combined make up amajority of the composition of the affinity reagent probes in the poolof affinity reagent probes. In some embodiments, a pool of affinityreagent probes may comprise 5 types of affinity reagent probes thatcombined make up a majority of the composition of the affinity reagentprobes in the pool of affinity reagent probes. In some embodiments, apool of affinity reagent probes may comprise more than 5 types ofaffinity reagent probes that combined make up a majority of thecomposition of the affinity reagent probes in the pool of affinityreagent probes. Each of the affinity reagent probes may be configured toselectively bind to one or more candidate proteins among the pluralityof candidate proteins. The affinity reagent probes may be k-mer affinityreagent probes. In some embodiments, each k-mer affinity reagent probeis configured to selectively bind to one or more candidate proteinsamong a plurality of candidate proteins. The information of empiricalmeasurements may comprise binding measurements of a set of probes thatare believed to have bound to an unknown protein.

Next, at least a portion of the information of empirical measurements ofan unknown protein may be compared, by the computer, against a databasecomprising a plurality of protein sequences (e.g., step 110). Each ofthe protein sequences may correspond to a candidate protein among theplurality of candidate proteins. The plurality of candidate proteins maycomprise at least 10, at least 20, at least 30, at least 40, at least50, at least 60, at least 70, at least 80, at least 90, at least 100, atleast 150, at least 200, at least 250, at least 300, at least 350, atleast 400, at least 450, at least 500, at least 600, at least 700, atleast 800, at least 900, at least 1000, or more than 1000 differentcandidate proteins.

Next, for each of one or more candidate proteins in the plurality ofcandidate proteins, a probability that an empirical measurement on thecandidate protein would generate an observed measurement outcome may becalculated or generated, by the computer (e.g., in step 115). The term“measurement outcome,” as used herein, refers to the informationobserved on performing a measurement. For example, the measurementoutcome of an affinity reagent binding experiment may be a positive ornegative outcome, such as either binding or non-binding of the reagent.As another example, the measurement outcome of an experiment measuringthe length of a protein may be 417 amino acids. Additionally, oralternatively, for each of one or more candidate proteins in theplurality of candidate proteins, a probability that an empiricalmeasurement on the candidate protein would not generate an observedmeasurement outcome, may be calculated or generated, by the computer.Additionally, or alternatively, a probability that an empiricalmeasurement on the candidate protein would generate an unobservedmeasurement outcome, may be calculated or generated by the computer.Additionally, or alternatively, a probability that a series of empiricalmeasurements on the candidate protein would generate an outcome set maybe calculated or generated, by the computer.

“Outcome set,” as used herein, refers to a plurality of independentmeasurement outcomes for a protein. For example, a series of empiricalaffinity reagent binding measurements may be performed on a unknownprotein. The binding measurement of each individual affinity reagentcomprises a measurement outcome, and the set of all measurement outcomesis the outcome set. In some cases, the outcome set may be a subset ofall observed outcomes. In some cases, the outcome set may consist ofmeasurement outcomes that were not empirically observed. Additionally oralternatively, for each of one or more candidate proteins in theplurality of candidate proteins, a probability that the unknown proteinis the candidate protein, may be calculated or generated, by thecomputer. The calculation or generation of steps 115 and/or 120 may beperformed iteratively or non-iteratively. The probabilities in step 115may be generated based on the comparison of the empirical measurementoutcomes of the unknown proteins against the database comprising theplurality of protein sequences for all candidate proteins. Thus, theinput to the algorithm may comprise a database of candidate proteinsequences and a set of empirical measurements (e.g., probes that arebelieved to have bound to an unknown protein, length of the unknownprotein, hydrophobicity of the unknown protein, and/or isoelectric pointof the unknown protein) for the unknown protein. In some cases, theinput to the algorithm may comprise parameters relevant to estimatingthe probability of any of the affinity reagents generating any bindingmeasurement for any of the candidate proteins (e.g. trimer-level bindingprobabilities for each affinity reagent). The output of the algorithmmay comprise (i) a probability that a measurement outcome or outcome setis observed given a hypothesized candidate protein identity, (ii) themost probable identity, selected from the set of candidate proteins, forthe unknown protein and the probability of that identification beingcorrect given a measurement outcome or outcome set (e.g., in step 120),and/or (iii) a group of high-probability candidate protein identitiesand an associated probability that the unknown protein is one of theproteins in the group. The probability that the measurement outcome isobserved given that a candidate protein is the protein being measuredmay be expressed as:P(measurement outcome|protein).

In some embodiments, P(measurement outcome|protein) is calculatedcompletely in silico. In some embodiments, P(measurementoutcome|protein) is calculated based on, or derived from, features ofthe amino acid sequence of the protein. In some embodiments,P(measurement outcome|protein) is calculated independent of knowledge ofthe amino acid sequence of the protein. For example, P(measurementoutcome|protein) may be determined empirically by acquiring themeasurement in replicate experiments on an isolate of the proteincandidate, and calculating the P(measurement outcome|protein) from thefrequency: (number of measurements with outcome/total number ofmeasurements). In some embodiments, P(measurement outcome|protein) isderived from a database of past measurements on the protein. In someembodiments P(measurement outcome protein) is calculated by generating aset of confident protein identifications from a collection of unknownproteins with the results of the measurement censored, and thencalculating the frequency of the measurement outcome among the set ofunknown proteins that were confidently identified as the candidateprotein. In some embodiments, a collection of unknown proteins may beidentified using a seed value of P(measurement outcome|protein), and theseed value refined based on the frequency of the measurement outcomeamong unknown proteins confidently matched to the candidate protein. Insome embodiments, this process is repeated, with new identificationsgenerated based on updated measurement outcome probabilities, and thennew measurement outcome probabilities generated from the updated set ofconfident identifications.

The probability that the measurement outcome is not observed given thata candidate protein is the protein being measured, may be expressed as:P(not measurement outcome|protein)=1−P(measurement outcome|protein).

The probability that a measurement outcome set consisting of Nindividual measurement outcomes is observed given that a candidateprotein is the protein being measured, may be expressed as a product ofthe probabilities for each individual measurement outcome:P(outcome set|protein)=P(measurement outcome 1|protein)*P(measurementoutcome 2|protein)* . . . *P(measurement outcome N|protein)

The probability of the unknown protein being a candidate protein(protein), may be calculated based on the probability of the outcome setfor each possible candidate protein.

In some embodiments, the measurement outcome set comprises binding ofaffinity reagent probes. In some embodiments, the measurement outcomeset comprises non-specific binding of affinity reagent probes.

In some embodiments, the protein in the sample is truncated or degraded.In some embodiments, the protein in the sample does not contain theC-terminus of the original protein. In some embodiments, the protein inthe sample does not contain the N-terminus of the original protein. Insome embodiments, the protein in the sample does not contain theN-terminus and does not contain the C-terminus of the original protein.

In some embodiments, the empirical measurements comprise measurementsperformed on mixtures of antibodies. In some embodiments, the empiricalmeasurements comprise measurements performed on samples containingproteins from a plurality of species. In some embodiments, the empiricalmeasurements comprise measurements performed on a sample derived fromhumans. In some embodiments, the empirical measurements comprisemeasurements performed on a sample derived from a different species thanhuman. In some embodiments, the empirical measurements comprisemeasurements performed on samples in the presence of single amino acidvariants (SAVs) caused by non-synonymous single-nucleotide polymorphisms(SNPs). In some embodiments, the empirical measurements comprisemeasurements on samples in the presence of genomic structural variation,such as insertions, deletions, translocations, inversions, segmentalduplications, or copy number variation (CNV) affecting the sequence ofthe proteins in the sample.

In some embodiments, the method further comprises applying the method toall unknown proteins measured in the sample. In some embodiments, themethod further comprises generating, for each of the one or morecandidate proteins, a confidence level that the candidate proteinmatches the unknown protein being measured in the sample. The confidencelevel may comprise a probability value. Alternatively, the confidencelevel may comprise a probability value with an error. Alternatively, theconfidence level may comprise a range of probability values, optionallywith a confidence (e.g., about 90%, about 95%, about 96%, about 97%,about 98%, about 99%, about 99.9%, about 99.99%, about 99.999%, about99.9999%, about 99.99999%, about 99.999999%, about 99.9999999%, about99.99999999%, about 99.999999999%, about 99.9999999999%, about99.99999999999%, about 99.999999999999%, about 99.9999999999999%confidence, or above 99.9999999999999% confidence).

In some embodiments, the method further comprises generating aprobability that a candidate protein is present in the sample.

In some embodiments, the method further comprises generating proteinidentifications, and associated probabilities, independently for eachunknown protein in the sample, and generating a list of all uniqueproteins identified in the sample. In some embodiments, the methodfurther comprises counting the number of identifications generated foreach unique candidate protein to determine the quantity of eachcandidate protein in the sample. In some embodiments, a collection ofprotein identifications and associated probabilities may be filtered toonly contain identifications of a high score, high confidence, and/orlow false discovery rate.

In some embodiments, binding probabilities may be generated for affinityreagents to full-length candidate proteins. In some embodiments, bindingprobabilities may be generated for affinity reagents to proteinfragments (e.g., a subsequence of the complete protein sequence). Forexample, if unknown proteins were processed and conjugated to thesubstrate in a manner such that only the first 100 amino acids of eachunknown protein were conjugated, binding probabilities may be generatedfor each protein candidate such that all binding probabilities forepitope binding beyond the first 100 amino acids are set to zero, oralternatively to a very low probability representing an error rate. Asimilar approach may be used if the first 10, 20, 50, 100, 150, 200,300, 400, or more than 400 amino acids of each protein are conjugated tothe substrate. A similar approach may be used if the last 10, 20, 50,100, 150, 200, 300, 400, or more than 400 amino acids are conjugated tothe substrate.

In some embodiments, in cases where a single protein candidate matchcannot be assigned to an unknown protein, a group of potential proteincandidate matches may be assigned to the unknown protein. A confidencelevel may be assigned to the unknown protein being one of any of theprotein candidates in the group. The confidence level may comprise aprobability value. Alternatively, the confidence level may comprise aprobability value with an error. Alternatively, the confidence level maycomprise a range of probability values, optionally with a confidence(e.g., about 90%, about 95%, about 96%, about 97%, about 98%, about 99%,about 99.9%, about 99.99%, about 99.999%, about 99.9999%, about99.99999%, about 99.999999%, about 99.9999999%, about 99.99999999%,about 99.999999999%, about 99.9999999999%, about 99.99999999999%, about99.999999999999%, about 99.9999999999999% confidence, or above99.9999999999999% confidence). For example, an unknown protein may matchstrongly with two protein candidates. The two protein candidates mayhave high sequence similarity to each other (e.g., two protein isoforms,such as proteins with single amino acid variants compared to a canonicalsequence). In these cases, no individual protein candidate may beassigned with high confidence, but a high confidence may be ascribed tothe unknown protein matching to a single, but unknown, member of the“protein group” comprising the two strongly matching protein candidates.

In some embodiments, efforts may be made to detect cases where unknownproteins are not optically-resolved. For example, on rare occasion, twoor more proteins may bind in the same “well” or location of a substratedespite efforts to prevent this occurrence. In some cases, theconjugated proteins may be treated with a non-specific dye and thesignal from the dye measured. In cases where two or more proteins arenot optically-resolved, the signal resulting from the dye may be higherthan locations containing a single protein and may be used to flaglocations with multiple bound proteins.

In some embodiments, the plurality of candidate proteins is generated ormodified by sequencing or analyzing the DNA or RNA of the human ororganism from which the sample of unknown proteins is obtained orderived.

In some embodiments, the method further comprises deriving informationon post-translational modifications of the unknown protein. Theinformation on post-translational modifications may comprise thepresence of a post-translational modification without knowledge of thenature of the specific modification. The database may be considered tobe an exponential product of PTMs. For example, once a protein candidatesequence has been assigned to an unknown protein, the pattern ofaffinity reagent binding for the assayed protein may be compared to adatabase containing binding measurements for the affinity reagents tothe same candidate from previous experiments. For example, a database ofbinding measurements may be derived from binding to a Nucleic AcidProgrammable Protein Array (NAPPA) containing unmodified proteins ofknown sequence at known locations.

Additionally or alternatively, a database of binding measurements may bederived from previous experiments in which protein candidate sequenceswere confidently assigned to unknown proteins. Discrepancies in bindingmeasurements between the assayed protein and the database of existingmeasurements may provide information on the likelihood ofpost-translation modification. For example, if an affinity agent has ahigh frequency of binding to the candidate protein in the database, butdoes not bind the assayed protein, there is a higher likelihood of apost-translational modification being present somewhere on the protein.If the binding epitope is known for the affinity reagent for which thereis a binding discrepancy, the location of the post translationalmodification may be localized to at or near the binding epitope of theaffinity reagent. In some embodiments, information on specificpost-translational modifications may be derived by performing repeatedaffinity reagent measurements before and after treatment of theprotein-substrate conjugate with an enzyme that specifically removes theparticular post translational modification. For example, bindingmeasurements may be acquired for a sequence of affinity reagents priorto treatment of the substrate with a phosphatase, and then repeatedafter treatment with a phosphatase. Affinity reagents which bind anunknown protein prior to phosphatase treatment but not after phosphatasetreatment (differential binding) may provide evidence ofphosphorylation. If the epitope recognized by the differentially bindingaffinity reagent is known, the phosphorylation may be localized to at ornear the binding epitope for the affinity reagent.

In some cases, the count of a particular post-translational modificationmay be determined using binding measurements with an affinity reagentagainst a particular post-translational modification. For example, anantibody that recognizes phosphorylation events may be used as anaffinity reagent. The binding of this reagent may indicate the presenceof at least one phosphorylation on the unknown protein. In some cases,the number of discrete post-translational modifications of a particulartype on an unknown protein may be determined by counting the number ofbinding events measured for an affinity reagent specific to theparticular post-translational modification. For example, aphosphorylation specific antibody may be conjugated to a fluorescentreporter. In this case, the intensity of the fluorescent signal may beused to determine the number of phosphorylation-specific affinityreagents bound to an unknown protein. The number ofphosphorylation-specific affinity reagents bound to the unknown proteinmay in turn be used to determine the number of phosphorylation sites onthe unknown protein. In some embodiments, evidence from affinity reagentbinding experiments may be combined with pre-existing knowledge of aminoacid sequence motifs or specific protein locations likely to bepost-translationally modified (e.g., from dbPTM, PhosphoSitePlus, orUniProt) to derive more accurate count, identification, or localizationof post-translational modification. For example, if the location of apost-translational modification is not exactly determined from affinitymeasurements alone, a location containing an amino acid sequence motiffrequently associated with the post translational modification ofinterest may be favored.

In some embodiments, the probabilities are iteratively generated until apredetermined condition is satisfied. In some embodiments, thepredetermined condition comprises generating each of the plurality ofprobabilities with a confidence of at least 50%, at least 55%, at least60%, at least 65%, at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, at least 99.9%, at least 99.99%, at least 99.999%, at least99.9999%, at least 99.99999%, at least 99.999999%, at least 99.9999999%,at least 99.99999999%, at least 99.999999999%, at least 99.9999999999%,at least 99.99999999999%, at least 99.999999999999%, at least99.9999999999999% confidence, or above 99.9999999999999% confidence.

In some embodiments, the method further comprises generating a paper orelectronic report identifying one or more unknown proteins in thesample. The paper or electronic report may further indicate, for each ofthe candidate proteins, a confidence level for the candidate proteinbeing present in the sample. The confidence level may comprise aprobability value. Alternatively, the confidence level may comprise aprobability value with an error. Alternatively, the confidence level maycomprise a range of probability values, optionally with a confidence(e.g., about 90%, about 95%, about 96%, about 97%, about 98%, about 99%,about 99.9%, about 99.99%, about 99.999%, about 99.9999%, about99.99999%, about 99.999999%, about 99.9999999%, about 99.99999999%,about 99.999999999%, about 99.9999999999%, about 99.99999999999%, about99.999999999999%, about 99.9999999999999% confidence, or above99.9999999999999% confidence). The paper or electronic report mayfurther indicate the list of protein candidates identified below anexpected false discovery rate threshold (e.g., a false discovery ratebelow 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.4%, 0.3%, 0.2%,or 0.1%). The false discovery rate may be estimated by first sorting theprotein identifications in descending order of confidence. The estimatedfalse discovery rate at any point in the sorted list may then becalculated as 1−avg_c_prob, where avg_c_prob is the average candidateprobability for all proteins at or before (e.g., higher confidence than)the current point in the list. A list of protein identifications below adesired false discovery rate threshold may then be generated byreturning all protein identifications before the earliest point in thesorted list where the false discovery rate is higher than the threshold.Alternatively, a list of protein identifications below a desired falsediscovery rate threshold may be generated by returning all proteinsbefore, and including, the latest point in the sorted list where thefalse discovery rate is below or equal to the desired threshold.

In some embodiments, the sample comprises a biological sample. Thebiological sample may be obtained from a subject. In some embodiments,the method further comprises identifying a disease state or a disorderin the subject based at least on the plurality of probabilities. In someembodiments, the method further comprises quantifying proteins bycounting the number of identifications generated for each proteincandidate. For example, the absolute quantity (e.g., number of proteinmolecules) of a protein present in the sample can be calculated bycounting the number of confident identifications generated from thatprotein candidate. In some embodiments, the quantity may be calculatedas a percentage of the total number of unknown proteins assayed. In someembodiments, the raw identification counts may be calibrated to removesystematic error from the instrument and detection systems. In someembodiments, the quantity may be calibrated to remove biases in quantitycaused by variation in detectability of protein candidates. Proteindetectability may be assessed from empirical measurements or computersimulation.

The disease or disorder may be an infectious disease, an immune disorderor disease, a cancer, a genetic disease, a degenerative disease, alifestyle disease, an injury, a rare disease or an age related disease.The infectious disease may be caused by bacteria, viruses, fungi and/orparasites. Non-limiting examples of cancers include Bladder cancer, Lungcancer, Brain cancer, Melanoma, Breast cancer, Non-Hodgkin lymphoma,Cervical cancer, Ovarian cancer, Colorectal cancer, Pancreatic cancer,Esophageal cancer, Prostate cancer, Kidney cancer, Skin cancer,Leukemia, Thyroid cancer, Liver cancer, and Uterine cancer. Someexamples of genetic diseases or disorders include, but are not limitedto, multiple sclerosis (MS), cystic fibrosis, Charcot-Marie-Toothdisease, Huntington's disease, Peutz-Jeghers syndrome, Down syndrome,Rheumatoid arthritis, and Tay-Sachs disease. Non-limiting examples oflifestyle diseases include obesity, diabetes, arteriosclerosis, heartdisease, stroke, hypertension, liver cirrhosis, nephritis, cancer,chronic obstructive pulmonary disease (copd), hearing problems, andchronic backache. Some examples of injuries include, but are not limitedto, abrasion, brain injuries, bruising, burns, concussions, congestiveheart failure, construction injuries, dislocation, flail chest,fracture, hemothorax, herniated disc, hip pointer, hypothermia,lacerations, pinched nerve, pneumothorax, rib fracture, sciatica, spinalcord injury, tendons ligaments fascia injury, traumatic brain injury,and whiplash.

In some embodiments, the method comprises identifying and quantifyingsmall molecules (e.g. metabolites) or glycans instead of, or in additionto, proteins. For example, affinity reagents, such as lectins orantibodies which bind to sugars or combinations of sugars with varyingpropensity, may be used to identify glycans. The propensity of theaffinity reagents to bind various sugars or combinations of sugars maybe characterized by analyzing binding to a commercially-available glycanarray. For example, unknown glycans may be conjugated to afunctionalized substrate using hydroxyl-reactive chemistry and bindingmeasurements may be acquired using the glycan-binding affinity reagents.The binding measurements of the affinity reagents to the unknown glycanson the substrate may be used directly to quantify the number of glycanswith a particular sugar or combination of sugars. Alternatively, one ormore binding measurements may be compared to predicted bindingmeasurements from a database of candidate glycan structures using themethods described herein to identify the structure of each unknownglycan. In some embodiments, proteins are bound to the substrate andbinding measurements with glycan affinity reagents are generated toidentify glycans attached to the proteins. Further, binding measurementsmay be made with both glycan and protein affinity reagents to generateprotein backbone sequence and conjugated glycan identifications in asingle experiment. As another example, metabolites may be conjugated toa functionalized substrate using chemistry targeted toward couplinggroups commonly found in metabolites such as sulfhydryl, carbonyl,amine, or active hydrogen. Binding measurements may be made usingaffinity reagents with different propensities to particular functionalgroups, structural motifs, or metabolites. The resulting bindingmeasurements may be compared to predicted binding measurements for adatabase of candidate small molecules, and the methods described hereinmay be used to identify the metabolite at each location on thesubstrate.

Example 1: Protein Identification by Affinity Reagent Binding

The methods described herein may be used in combination with affinitybinding reagents (e.g., aptamers or antibodies) binding measurements toanalyze and/or identify proteins in a sample. In this case, themeasurement outcome probability to be calculated is the probability of abinding or non-binding event of an affinity binding reagent (e.g.,affinity reagent or affinity probe) to a protein candidate. A bindingprobability may be modeled as being conditional on the presence of anepitope which is recognized by the affinity binding reagent beingpresent in the sequence of the protein. For example, an epitope may be a“trimer” (a sequence of three amino acids). An affinity reagent may bedesigned to target a particular epitope (e.g., GAV). Off-target bindingof an affinity reagent (e.g., binding of an affinity reagent to anepitope different from its target epitope) may be modeled by including anon-zero probability of binding to additional epitopes.

For example, an affinity reagent may be designed to bind the GAV trimer,but may have off-target binding to three additional recognition sites:CLD, TYL, and IAD. For this affinity reagent, the binding probabilitycan be modeled as:P(affinity probe binding|protein)={0.25, if GAV, CLD, TYL, or IAD ispresent in the protein sequence;0, otherwise}.

There may also be a small probability of the affinity reagent bindingnon-specifically to a protein, which can be expressed as: P(affinityprobe binding|protein)={0.25, if GAV, CLD, TYL, or IAD is present in theprotein sequence; 0.00001, otherwise}. Here, the probability measuresthe outcome of the detection of antibody binding.

As an example, consider a case where proteins from a human-derivedsample are analyzed. The proteins in the sample are assumed to berepresented in the human “reference” proteome (for example, as found inthe Uniprot database of canonical protein sequence and functionalinformation). That is, the protein candidate list is the set of about 21thousand proteins and associated sequences in the UniProt database. Acollection of unknown proteins are derived from the sample, and eachunknown protein is probed in a series of affinity reagent bindingexperiments with the outcome (binding or no binding) measured andrecorded. For example, such experiments may comprise sequentially addingdifferent affinity reagents and observing the binding of the affinityreagents to the unknown proteins. The affinity reagents, or “probes,”are selected to target the most frequently observed trimers (out ofabout 800 possible trimers) in the protein candidate list. Outside ofthe targeted trimer, each probe has off-target binding to a number ofadditional trimers which are selected at random. The probability of aprobe binding to a protein sequence can be expressed as:P(affinity probe binding|protein)=1−[P(no non-specific binding)*_(P)(nospecific binding)].

Assuming that:

n=sequence length of a protein candidate; q=length of a recognition site(e.g., 3);

s=non-specific trimer binding probability (e.g., 10⁻⁵); p=specificbinding probability (e.g., 0.25); the terms P(no non-specific binding)and P(no specific binding) can be expressed as:P(no non-specific binding)=(1−s)^(n−q+1)=(1−10⁻⁵)^(n−3+1)and P(no specificbinding)=Π_(for each recognition site)(1−p)^(number of site occurrences in protein).

Finally, the probability of a probe not binding to a protein can beexpressed as:P(affinity probe not binding|protein)=1−P(affinity probebinding|protein).

FIG. 2 illustrates the sensitivity of affinity reagent probes (e.g., thepercent of substrates identified with a false detection rate (FDR) ofless than 1%) plotted against the number of probe recognition sites(e.g., trimer-binding epitopes) in the affinity reagent probe (rangingup to 100 probe recognition sites or trimer-binding epitopes), for threedifferent experimental cases (with 50, 100, and 200 probes used, asdenoted by the gray, black, and white circles, respectively). As seen inFIG. 2, the number of probes used has a significant effect on theability to correctly identify proteins. Plotted on the y-axis is thesensitivity, which is the percentage of the unknown proteins that arecorrectly identified with a threshold (e.g., upper limit) of less than1% of the identifications being incorrect. For example, if each probecontains 5 recognition sites or trimer-binding epitopes (1 targeted siteand 4 off-target sites), the sensitivity of protein identification isless than 10% when 50 probes are used, about 60% when 100 probes areused, and about 90% when 200 probes are used. In fact, when 300 probesare used, the sensitivity exceeds 95% (result not shown on plot). Thisprotein identification approach supports probes with many off-targetbinding sites. Even with 60 recognition sites or trimer-binding epitopes(1 targeted site and 59 off-target sites), identification sensitivity isabout 55% in a 100-probe experiment and about 90% in a 200-probeexperiment.

However, as seen in FIG. 3, the ability to identify proteins degradesrapidly when probes have more than 100 binding sites or trimer-bindingepitopes. FIG. 3 illustrates the sensitivity of affinity reagent probes(e.g., the percent of substrates identified with a false detection rate(FDR) of less than 1%) plotted against the number of probe recognitionsites (e.g., trimer-binding epitopes) in the affinity reagent probe(ranging up to 700 probe recognition sites or trimer-binding epitopes)for three different experimental cases (with 50, 100, and 200 probesused, as denoted by the gray, black, and white circles, respectively).For example, if each probe contains 100 recognition sites ortrimer-binding epitopes (1 targeted site, 99 off-target sites), thesensitivity of protein identification is about 1% when 50 probes areused, about 30% when 100 probes are used, and about 70% when 200 probesare used. However, if each probe contains 200 recognition sites ortrimer-binding epitopes (1 targeted site, 199 off-target sites), thesensitivity of protein identification is less than 1% when 50 probes areused, less than 20% when 100 probes are used, and less than 40% when 200probes are used.

Example 2: Protein Affinity Reagent Binding to Proteins that have beenTruncated or Degraded

The methods described herein may be applied to analyze and/or identifyproteins in a sample that have been truncated. In such experiments,probability calculation of an affinity probe binding to a protein ismodified to only consider binding to the truncated protein sequence,rather than the full protein sequence. For example, FIG. 4 illustratesplots showing the sensitivity of protein identification with experimentsusing 100 (left), 200 (center), or 300 probes (right). In each plot,sensitivity of affinity reagent probes (e.g., the percent of substratesidentified with a false detection rate (FDR) of less than 1%) isdetermined for an experiment in which 4 substrates lengths are measured:(1) the intact (full) protein, (2) the 50-length N- or C-terminalfragment of the protein, (3) the 100-length N- or C-terminal fragment ofthe protein, and (4) the 200-length N- or C-terminal fragment of theprotein. N- and C-terminal fragments are denoted with solid and stripedbars, respectively. Each probe binds to the targeted trimer and 4 otherrandom off-target trimers. As shown in FIG. 4, a substantial proportionof proteins (˜40%) may be identified, for example, even when proteinsare truncated to fragments containing only 100 amino acids and 200-probeexperiments are performed.

If 300 probes are used, then about 70-75% of proteins may be identifiedin the case when proteins are truncated to fragments containing only 100amino acids. FIG. 4 also shows that truncated proteins containing theN-terminal fragment are slightly easier to identify (e.g., with highersensitivity of protein identification) than fragments containing theC-terminal fragment.

Example 3: Protein Fragments Containing Neither the C-Terminus Nor theN-Terminus of the Intact Protein from which they are Derived

The methods described herein may be applied to analyze and/or identifyprotein fragments in a sample that contain neither of the original 2termini of the intact protein from which the fragment is derived. Theprobability calculation of an affinity probe binding to a protein insuch an experiment is modified to only consider binding to the truncatedrather than the full protein sequence. FIG. 5 illustrates plots showingthe sensitivity of protein identification with experiments using variousprotein fragmentation approaches. In each of the top row and the bottomrow, protein identification performance is shown with 50, 100, 200, and300 affinity reagent measurements (in the 4 panels from left to right),with maximum fragment length values of 50, 100, 200, 300, 400, and 500(as denoted by the hexagons, down-pointing triangles, up-pointingtriangles, diamonds, rectangles, and circles, respectively).

Referring to the top row of FIG. 5, each point on each subplotrepresents sensitivity (protein identification rate) when using aparticular fragment generation approach defined by the fragment startlocation and fragment length. Fragments are generated at a specificstarting location on each protein indexed by distance (e.g., number ofamino acids (AA) away) from the N-terminus in amino acids (as plotted onthe x-axis). The end of each protein fragment is selected to generate afragment with length 50, 100, 200, 300, 400, or 500 amino acids (maximumfragment length, or max_fragment_length values), as denoted by thehexagons, down-pointing triangles, up-pointing triangles, diamonds,rectangles, and circles, respectively. If a fragment of a givendesignated length cannot be generated because the protein is too short,the fragment shorter than the requested length containing the C-terminusis retained. For example, when an experiment is performed with 50affinity reagents, only a small percentage of proteins may be identified(as plotted on the y-axis). However, when an experiment is performedwith 200 affinity reagent probes using fragments with a maximum lengthof 200 amino acids, about 50% to about 85% of proteins may be identified(as plotted on the y-axis) depending on the fragment start site (asplotted on the x-axis). There is a general trend of decrease in proteinidentification sensitivity as the fragment start site moves further awayfrom the N-terminus. This trend can be explained by the fact that, asthe fragment start moves farther from the N-terminus, more fragments aregenerated that include the C-terminus and are less than the maximumfragment length.

Referring to the bottom row of FIG. 5, the 4 subplots here show similarresults as those in the top row, except that any fragments which do notmatch the maximum fragment length (e.g., fragments not containing theC-terminus) are discarded from analysis prior to the sensitivity andfalse discovery rate calculation. The sensitivity of proteinidentification is calculated only among those proteins that may havegenerated a valid fragment. As the bottom row of FIG. 5 shows, withoutthe fragment length fixed, at the maximum fragment length, there is nostatistically significant variation in protein identificationsensitivity with respect to the location of the fragment start site.Fragment length is the major determinant of protein identification raterather than the fragment location within the protein sequence.

Example 4: Protein Identification by Measurement of Length,Hydrophobicity, and/or Isoelectric Point

The methods described herein may be applied to analyze and/or identifyproteins in a sample using information from measurements on theproteins, including length, hydrophobicity, and/or isoelectric point(pI). The probability of measuring a particular length for a proteinquery candidate can be expressed by:

${P\left( {{measurement}\mspace{14mu}{outcome}} \middle| {protein} \right)} = {\frac{1}{\sigma\sqrt{2\pi}}{\exp\left( {- \frac{u^{2}}{2}} \right)}\mspace{14mu}{where}}$σ = CV^(*)  expected  outcome  valueu = (measured  outcome  value − expected  outcome  value)/σ

In this case, the measurement outcome is the measured length of theunknown protein, and the expected outcome value is the length of theprotein query candidate. The model also uses a coefficient of variation(CV) value which describes the expected precision of the measurementapproach. The probability of measuring a particular hydrophobicity for aprotein is calculated using the same formula, with the expected outcomevalue being set to a grand average of hydropathy (gravy) scorecalculated from the protein candidate sequence. Such a gravy score canbe calculated, for example, using a Biopython tool for computationalmolecular biology to perform a Kyte-Doolittle computational method(e.g., as described in [Kyte et al., “A simple method for displaying thehydropathic character of a protein,” J. Mol. Biol., 1982 May 5;157(1):105-32], which is incorporated herein by reference in itsentirety). Similarly, isoelectric point (pI) is modeled with an expectedpI value calculated from the protein candidate sequence using Biopythonto implement the methods of Bjellqvist (e.g., as described in [Audain etal., “Accurate estimation of isoelectric point of protein and peptidebased on amino acid sequences,” Bioinformatics, 2015 Nov. 14;32(6):821-.27], which is incorporated herein by reference in itsentirety), according to the methods described in [Tabb, David L., “Analgorithm for isoelectric point estimation,”<http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf>, 2003Jun. 28], which is incorporated herein by reference in its entirety. Inall cases, the experimental measurement precision was set to a CV valueof 0.1.

FIG. 6 illustrates plots showing the sensitivity of identification ofhuman proteins (percent of substrates identified at an FDR of less than1%) with experiments using various combinations of types ofmeasurements. Using protein length, hydrophobicity, or pI measurementsalone, virtually no proteins can be identified (e.g., a sensitivity<1%).Combining all three types of measurements (len+hydro+pI) still yieldsvirtually no identifications. However, protein length, hydrophobicity,or pI measurements may be used to augment measurements from affinityreagent probe binding experiments. For example, proteins may befractionated based on any of these characteristics, and each fractionconjugated to a different spatial location on the substrate. Followingthis fractionation and conjugation, affinity reagent bindingmeasurements may be made, and the measurement of hydrophobicity, proteinlength, or pI may be determined by the spatial address of the protein.Denatured proteins may be fractionated by molecular weight based on gelfiltration (SDS-PAGE) or size exclusion chromatography. The length ofproteins may be estimated from the molecular weight by dividing theweight by the average mass of an amino acid (111 Da). Proteins may befractionated by hydrophobicity using hydrophobic interactionchromatography. Proteins may be fractionated by pI using ion exchangechromatography. For example, performing additional measurements ofprotein length by fractionation with a CV value of 0.1 improvedsensitivity of identification using 100-probe (1 targeted trimer, and 4additional off-target sites per probe) experiments from ˜55% (withoutprotein length measurements) to ˜65% (with protein length measurements).Similarly, performing additional measurements of protein length with aCV value of 0.1 improved sensitivity of identification using 200-probe(1 targeted trimer, and 4 additional off-target sites per probe)experiments from ˜90% (without protein length measurements) to ˜95%(with protein length measurements).

Example 5: Protein Identification by Measurement with Mixtures ofAntibodies

The methods described herein may be applied to analyze and/or identifyproteins in a sample using information from experiments in whichmixtures of affinity reagents are measured in each binding experiment.Consistent with disclosed embodiments, the identification of 1,000unknown human proteins was benchmarked by acquiring binding measurementsusing pools of commercially-available antibodies from Santa CruzBiotechnology, Inc. The 1,000 proteins were randomly selected from theUniprot protein database, which comprises about 21,005 proteins. A listof monoclonal antibodies available from the Santa Cruz Biotechnologycatalog with reactivity against human proteins was downloaded from anonline antibody registry. The list contained 22,301 antibodies and wasfiltered to a list of 14,566 antibodies which matched to proteins in theUniprot human protein database. The complete collection of antibodiesmodeled in the experiment comprised these 14,566 antibodies.Experimental assessment of binding of antibody mixtures to the 1,000unknown protein candidates was performed as described below.

First, 50 mixtures of antibodies were modeled. To produce any singlemixture, 5,000 antibodies from the total collection of antibodies wereselected at random.

Next, for each mixture, a binding probability was determined for themixture to any of the unknown proteins. Note that, although the proteinsare “unknown” in the sense that the goal is to infer their identity, thealgorithm is aware of the true identity of each “unknown protein.” Ifthe mixture contains an antibody against the unknown protein, a bindingprobability of 0.99 was assigned. If the mixture does not contain anantibody against the unknown protein, a binding probability of 0.0488was assigned. In other words, the probability of a binding outcome forthe mixture of antibodies was modeled as: P(bindingoutcome|protein)={0.99, if mixture contains an antibody to the protein;0.0488, otherwise}. The value of 0.0488 represents the probability of anon-specific (off-target) binding event occurring for this mixtureagainst the protein. The non-specific binding probability for a mixturewas modeled based on the expected probability of any individual antibodybinding a protein other than its target, and the number of proteins inthe mixture. The probability of a non-specific binding event for themixture of antibodies is the probability of any single antibody in themixture binding non-specifically. This probability is calculated basedon the number of antibodies in the mixture (n), and the probability ofnon-specific binding (p) for any single antibody, and can be expressedby the equation:Mixture non-specific binding probability=1−(1−p)^(n)

In this case, it was assumed that there is a probability of 0.00001(10⁻⁵) of a non-specific binding event where an individual antibodybinding something other than its target protein. Therefore, thenon-specific binding probability (p) for any single antibody is 10⁻⁵,giving: Mixture non-specific binding probability=1−(1−10⁻⁵)⁵⁰⁰⁰=0.0488.

In addition, the probability of a non-binding outcome to a protein wascalculated as:P(non-binding outcome|protein)=1−P(binding outcome|protein).

For each unknown protein, binding was assessed for each antibody mixturemeasured based on the binding probability of the mixture to the unknownprotein. The uniform distribution, with a minimum of 0 and a maximum of1, was randomly sampled, and if the resulting number is less than thebinding probability of the antibody mixture to the unknown protein, theexperiment resulted in a binding event for that mixture. Otherwise, theexperiment resulted in a non-binding event for that mixture. With allbinding events assessed, protein inference is performed as follows:

For each unknown protein, the sequence of assessed binding events (50total, 1 per mixture) was evaluated against each of the 21,005 proteincandidates in the Uniprot database. More specifically, a probability ofobserving the sequence of binding events was calculated for eachcandidate. The probability was calculated by multiplying the probabilityof each individual mixture binding/non-binding event across all 50mixtures measured. The binding probability was calculated in the samemanner as described above, and the probability of non-binding is oneminus the binding probability. The protein query candidate with thehighest binding probability is the inferred identity for the unknownprotein. A probability of the identification being correct for thatindividual protein was calculated as the probability of the topindividual candidate divided by the summed probabilities of allcandidates.

With the identity inferred for each of the 1,000 unknown proteins, theunknown proteins were sorted in descending order of their identificationprobability. An identification probability cutoff was selected such thatthe percentage of incorrect identifications among all identificationsprior in the list was 1%. Overall, 551 of the 1,000 unknown proteinswere identified with a 1% incorrect identification rate. Therefore,protein identification was performed with a sensitivity of 55.1%.

Example 6: Protein Identification in Many Species

The methods described herein may be applied to analyze and/or identifyproteins in a sample obtained from many different species. For example,results from sequence of affinity reagent binding experiments may beused to identify proteins in E. coli, Saccharomyces cerevisiae (yeast),or Homo sapiens (humans), as denoted by the circles, triangles, andsquares, respectively. To adapt analytical methods for each species, theprotein candidate list must be generated from a species-specificsequence database, such as a reference proteome for the speciesdownloaded from Uniprot.

FIG. 7 illustrates plots showing the sensitivity of proteinidentification with experiments using 50, 100, 200, or 300 affinityreagent probe passes against unknown proteins from either E. coli,yeast, or human (as denoted by the circles, triangles, and squares,respectively). Each probe binds to a targeted trimer, and 4 additionaloff-target sites with probability of 0.25. The sensitivity (percentageof unknown proteins identified at a false identification rate of lessthan 1%) for an experiment using 200 probes was about 90% for each ofthe three species tested.

Example 7: Protein Identification in the Presence of SNPs

The methods described herein may be applied to analyze and/or identifyproteins in a sample in the presence of single amino acid variants(SAVs) caused by non-synonymous single-nucleotide polymorphisms (SNPs).Proteins that have the same sequence except for a handful of singleamino acid variants (SAVs) may be difficult to distinguish. For example,in an experiment using a series of affinity reagent measurements, thecanonical form of a protein may be nearly impossible to distinguish fromits variant form, unless an affinity reagent which is highly-selectivefor the polymorphic region of the protein is included in the experiment.In cases where the polymorphic region is not distinguished by any of theaffinity reagent measurements, measurements of either protein form willreturn similar probabilities (likelihoods) for both the canonical andvariant protein query candidate (e.g., L(canonical protein|evidence)=0.8and L (variant protein|evidence)=0.8).

In such a case, neither individual protein candidate may return aprobability higher than 0.5, e.g., as expressed for the canonicalprotein below (where cprot=canonical protein, vprot=variant protein):

${P{r\left( {cprot} \middle| {evidence} \right)}} = {\frac{L\left( {cprot} \middle| {evidence} \right)}{{L\left( {cprot} \middle| {evidence} \right)} + {L\left( {vprot} \middle| {evidence} \right)} + L_{other}} = {\frac{0.8}{{1.6} + L_{other}} \leq {0.5}}}$where L_(other) is the summed likelihood of all protein query candidatesexcept the canonical protein and the variant protein and is a numbergreater than or equal to zero.

In this case, groups of potential protein identifications may bereturned for an unknown protein. For example, the probability for thetop two most likely protein query candidates may be expressed as:

${P{r\left( {{cprot}\mspace{14mu}{or}\mspace{14mu}{vprot}} \middle| {evidence} \right)}} = {\frac{{L\left( {cprot} \middle| {evidence} \right)} + {L\left( {vprot} \middle| {evidence} \right)}}{{L\left( {cprot} \middle| {evidence} \right)} + {L\left( v \middle| {evidence} \right)} + L_{other}} = \frac{1.6}{{1.6} + L_{other}}}$Using this approach, a confident identification may be derived from theunknown protein, albeit one that does not resolve the canonical proteinand the variant protein. In particular, cases where L_(other) is nearzero may be likely to result in a confident identification.

Example 8: Iterative Improvement of Probability Model from EmpiricalResults

A probabilistic model used in one or more methods described herein maybe improved iteratively using empirical measurements during thecomputation of protein identifications using expectation maximization orrelated approaches. One such approach is described here for an affinityreagent binding experiment.

First, the binding probabilities for each affinity reagent probe areinitialized with an estimate. For example, a collection of 200 probesmay each target a single trimer and have an estimated bindingprobability of 0.5. Proteins are identified using the approachesdisclosed elsewhere herein (for example, see Example 1). Next, thebinding probabilities for each probe are refined iteratively based onempirical measurements, as summarized by the steps below:

(1) Use the collection of unknown proteins identified with estimatedfalse discovery rate<0.01 to update binding probabilities:

For each probe, calculate the updated binding probability using theproportion of proteins

-   -   in the collection that contain a binding site (trimer)        recognized by the probe:

${{updated}\mspace{14mu}{probability}} = \frac{\begin{matrix}{\sharp\mspace{14mu}{of}\mspace{14mu}{proteins}\mspace{14mu}{in}\mspace{20mu}{collection}\mspace{14mu}{with}\mspace{14mu}{b{inding}}} \\{{site}\mspace{14mu}{that}\mspace{14mu}{are}\mspace{14mu}{bound}\mspace{14mu}{by}\mspace{14mu}{the}\mspace{14mu}{probe}}\end{matrix}}{\sharp\mspace{14mu}{of}\mspace{14mu}{proteins}\mspace{14mu}{in}\mspace{14mu}{collection}\mspace{14mu}{with}\mspace{14mu}{binding}\mspace{20mu}{site}}$

Update the probe probability of “# of proteins in collection withbinding site>20”.

If the updated probability is <10⁻⁵, set it to 10⁻⁵ (to avoid aprobability of 0 being assigned).

(2) Perform another protein identification using the updated bindingprobabilities.

Repeat steps 1 and 2 for multiple iterations (e.g., for a total of 1, 2,3, 4, 5, 6, 7, 8, 9, 10, or more than 10 iterations).

This iterative approach was tested using an experiment with 200 probes,each recognizing a single trimer with binding probability of 0.25. The200 probe binding measurements were modeled against 2000 unknownproteins with the initial estimate for the probe binding probability setto 0.5. After performing 5 iterations of this iterative algorithm, theupdated probe binding probabilities became more accurate (closer to0.25) and the protein identification sensitivity increased.

FIG. 8 illustrates a plot showing the binding probability (y-axis, left)and sensitivity of protein identification (y-axis, right) againstiteration (x-axis). As shown in FIG. 8, thin lines show the probebinding probabilities for each individual probe, the dark line among thethin lines is the median probe binding probability, and the thick lineshows the protein identification sensitivity at each iteration.

Example 9: Estimating Identification False Discovery Rate from ProteinCandidate Match Probabilities

A probabilistic model for protein inference or identification used inone or more methods described herein yields as direct results a list ofprotein sequence matches for each unknown protein and an associatedprobability of that sequence match being correct. In many cases, only asubset of the protein identifications may be correct. Therefore, amethod useful for estimating and controlling the false identificationrate for a set of proteins is described below.

First, the complete set of protein identifications is sorted indescending order by the protein identification probability, as givenbelow (where prot=protein):

prot1 probability (p₁): 0.99

prot2 probability (p₂): 0.97

prot3 probability (p₃): 0.92

prot4 probability (p₄): 0.9

prot5 probability (p₅): 0.8

prot6 probability (p₆): 0.75

prot7 probability (p₇): 0.6

prot8 probability (p₈): 0.5

Next, the expected false discovery rate at each point in the list iscalculated as 1−p where p is the average of all probabilities at thegiven point and earlier in the list (as given below):

Protein Probability Estimated False ID Rate prot1 0.990 0.010 prot20.970 0.020 prot3 0.920 0.040 prot4 0.900 0.055 prot5 0.800 0.084 prot60.750 0.112 prot7 0.600 0.153 prot8 0.500 0.196

As shown in FIG. 9, a comparison of the estimated false identificationrate to the true false identification rate for a simulated 200-probeexperiment demonstrates accurate false identification rate estimation.Referring to the top plot of FIG. 9, identification sensitivity iscompared to the true false identification rate and the estimated falseidentification rate. Referring to the bottom plot of FIG. 9, theestimated false identification rate is plotted against the true falseidentification rate (as indicated by the solid line), while the dashedline indicates an ideal perfectly accurate false identification rateestimation.

The estimated false identification (ID) rate may be used to threshold alist of protein identifications depending on a tolerance for falseidentifications.

Example 10: Derivation of a False Discovery Rate Estimation Approach

Consider a list of protein identifications, each protein identificationcomprising the most likely protein match for an unknown protein, and theassociated probability of that match being correct (P(protein|evidence).For example:

prot₁—MACD2, p₁=0.99

prot₂—KCNU1, p₂=0.97

prot₃—RGL2, p₃=0.92

prot₄—MTLR, p₄=0.9

The expected number of false discoveries in this list is 1−the averagematching probability for all proteins in the list. In this case:

${1 - \frac{{{0.9}9} + {{0.9}7} + {{0.9}2} + {0.9}}{4}} = {{0.0}55}$

The rationale behind this approach is as follows. Consider a list of Nprotein identifications, and each protein identification prot_(i) to bea random variable where prot_(i)=1 if the identification is correct andprot_(i)=0 if the identification is incorrect. In this case, the numberof correct identifications (correctids) in any list is the sum of theserandom variables:

${correctids} = {\sum\limits_{i = 1}^{N}{prot}_{i}}$

The expectation value for each individual protein identification isequivalent to the probability of a correct identification:E(prot_(i))=1*p _(i)+0*(1−p _(i))=p _(i)

By linearity of expectation, it follows that:

${E({correctids})} = {{\sum\limits_{i = 1}^{N}{E\left( {prot}_{i} \right)}} = {\sum\limits_{i = 1}^{N}p_{i}}}$

The expected true discovery rate (#correct IDs/#IDs) is the averagecandidate probability:

$\frac{E({correctids})}{N} = {{\frac{1}{N}{\sum\limits_{i = 1}^{N}p_{i}}} = \overset{\_}{p}}$

The false discovery rate is 1−true discovery rate, or:1−{tilde over (p)}

Example 11: Protein Identification Using Binding Measurement Outcomes

The methods described herein may be applied to different subsets of dataassociated with the binding and/or non-binding of affinity reagents tounidentified proteins. In some embodiments, methods described herein maybe applied to experiments in which a particular subset of the measuredbinding outcomes is not considered (e.g., non-binding measurementoutcomes). These methods where a subset of the measured binding outcomesare not considered may be referred to herein as a “censored” inferenceapproach (e.g., as described in Example 1). In the results described inFIG. 10, the protein identifications that result from the censoredinference approach are based on assessing occurrences of binding eventsassociated with the particular unidentified proteins. Accordingly, thecensored inference approach does not consider non-binding outcomes indetermining identities of unknown proteins.

This type of censored inference approach is in contrast to an“uncensored” approach, in which all obtained binding outcomes areconsidered (e.g., both binding measurement outcomes and non-bindingmeasurement outcomes associated with the particular unidentifiedproteins). In some embodiments, a censored approach may be applicable incases where there is an expectation that particular binding measurementsor binding measurement outcomes are more error-prone or likely todeviate from the expected binding measurement outcome for the protein(e.g. the probability of that binding measurement outcome beinggenerated by the protein). For example, in an affinity reagent bindingexperiment, probabilities of binding measurement outcomes andnon-binding measurement outcomes may be calculated based on binding todenatured proteins with predominantly linear structure. In theseconditions, epitopes may be easily accessible to affinity reagents.However, in some embodiments, binding measurements on the assayedprotein sample may be collected under non-denaturing orpartially-denaturing conditions where proteins are present in a “folded”state with significant 3-dimensional structure, which can in many casescause affinity reagent binding epitopes on the protein that areaccessible in a linearized form to be inaccessible due to sterichindrance in the folded state. If, for example, the epitopes that theaffinity reagent recognizes for a protein are in structurally accessibleregions of the folded protein, the expectation may be that empiricalbinding measurements acquired on the unknown sample will be consistentwith the calculated probabilities of binding derived from linearizedproteins. However, if, for example, the epitopes recognized by theaffinity reagent are structurally inaccessible, the expectation may bethat there will be more non-binding outcomes than expected fromcalculated probabilities of binding derived from linearized proteins.Further, based on the particular conditions surrounding the protein, the3-dimensional structure may be configured in a number of differentpossible configurations, and each of the different possibleconfigurations may have an unique expectation for binding a particularaffinity reagent based on the degree of accessibility of the desiredaffinity reagent.

As such, non-binding outcomes may be expected to deviate from thecalculated binding probabilities for each protein, and a censoredinference approach which only considers binding outcomes may beappropriate. In the “censored” inference approach as provided in FIG.10, only measured binding outcomes are considered (in other words,either non-binding outcomes are not measured, or measured non-bindingoutcomes are not considered), such that the probability of a bindingoutcome set only considers the M measured binding outcomes that resultedin a binding measurement, which is a subset of the N total measuredbinding outcomes containing both binding and non-binding measurementoutcomes. This may be described by the expression:P(outcome set|protein)=P(binding event 1|protein)*P(binding event2|protein)* . . . *P(binding event M|protein)

When applying a censored approach, it may be appropriate to apply ascaling factor to P(binding outcome set protein) to correct for biases.For example, longer proteins generally have a higher probability ofgenerating a potential binding outcome (e.g., because they contain morepotential binding sites). To correct for this bias, a scaled likelihoodSL may be calculated for each candidate protein by dividing theP(binding outcome set protein) by the number of unique combinations of Mbinding sites that can be generated from the protein based on the numberof potential binding sites on the protein. For a protein of length L,with trimer recognition sites, there may be L−2 potential binding sites(e.g., every possible length L subsequence of the complete proteinsequence), such that:

${SL}_{Protein} = {\frac{P\left( {{outcome}\mspace{14mu}{set}} \middle| {protein} \right)}{\begin{pmatrix}{L - 2} \\M\end{pmatrix}} = \frac{{P\left( {{outcome}\mspace{14mu}{set}} \middle| {protein} \right)}M{!{\left( {L - 2 - M} \right)!}}}{\left( {L - 2} \right)!}}$

The probability of any candidate protein selected from a collection of Qpossible candidate proteins, given the outcome set, may be given by:

${P\left( {protein}_{i} \middle| {{outcome}\mspace{14mu}{set}} \right)} = \frac{{SL}_{{Protein}_{i}}}{\sum\limits_{j = 1}^{Q}{SL}_{{Protein}_{j}}}$

The performance of an embodiment of a censored protein inference vs.uncensored protein inference approach is plotted in FIG. 10. The dataplotted in FIG. 10 is provided in Table 1.

TABLE 1 Number of Censored Probes Sensitivity TRUE 100 1.52 FALSE 10056.84 TRUE 200 73.28 FALSE 200 93.18 TRUE 300 93.92 FALSE 300 98.14 TRUE400 96.68 FALSE 400 98.84 TRUE 500 98.42 FALSE 500 99.6

In the comparison shown in FIG. 10, the protein identificationsensitivity (e.g., percent of unique proteins identified) is plottedagainst the number of affinity reagent cycles measured for both censoredinference and uncensored inference used on linearized proteinsubstrates. The affinity reagents used are targeted against the top mostabundant trimers in the proteome, and each affinity reagent hasoff-target affinity to four additional random trimers. The uncensoredapproach outperforms the censored approach by a greater than ten-foldmargin when 100 affinity reagent cycles are used. The degree to whichuncensored inference outperforms censored inference lessens when morecycles are used.

Example 12: Tolerance of Protein Identification to Random False Negativeand False Positive Affinity Reagent Binding

In some cases, there may be a high incidence of false negative bindingmeasurement outcomes for affinity reagent binding. “False negative”binding outcomes manifest as affinity reagent binding measurementsoccurring less frequently than expected. Such “false negative” outcomesmay arise, for example, due to issues with the binding detection method,the binding conditions (for example, temperature, buffer composition,etc.), corruption of the protein sample, or corruption of the affinityreagent stock. To determine the impact of false negative measurements onthe censored protein identification and the uncensored proteinidentification approach, a subset of affinity reagent measurement cycleswere purposely corrupted by switching either 1 in 10, 1 in 100, 1 in1,000, 1 in 10,000, or 1 in 100,000 random observed binding events tonon-binding events in silico. Either 0, 1, 50, 100, 200, or 300 of the300 total affinity reagent cycles were corrupted in this manner. Asshown by the results plotted in FIG. 11, both the censored proteinidentification approach and the uncensored protein identificationapproach are tolerant to this type of random false negative binding. Thedata plotted in FIG. 11 is provided in Table 2.

TABLE 2 False Number of Negative Number of Probes Censored Rate ProbesImpacted Sensitivity TRUE 0.1 300 0 93.32 FALSE 0.1 300 0 98.04 TRUE 0.1300 1 93.42 FALSE 0.1 300 1 98.12 TRUE 0.01 300 1 92.98 FALSE 0.01 300 198.48 TRUE 0.001 300 1 92.8 FALSE 0.001 300 1 97.82 TRUE 0.0001 300 192.82 FALSE 0.0001 300 1 98.32 TRUE 0.00001 300 1 93.38 FALSE 0.00001300 1 98.02 TRUE 0.1 300 50 92.26 FALSE 0.1 300 50 97.96 TRUE 0.01 30050 92.7 FALSE 0.01 300 50 97.76 TRUE 0.001 300 50 93.72 FALSE 0.001 30050 98.04 TRUE 0.0001 300 50 92.96 FALSE 0.0001 300 50 97.84 TRUE 0.00001300 50 93.7 FALSE 0.00001 300 50 98.1 TRUE 0.1 300 100 92.38 FALSE 0.1300 100 97.66 TRUE 0.01 300 100 93.02 FALSE 0.01 300 100 97.7 TRUE 0.001300 100 92.48 FALSE 0.001 300 100 97.96 TRUE 0.0001 300 100 93.74 FALSE0.0001 300 100 98.34 TRUE 0.00001 300 100 91.88 FALSE 0.00001 300 10097.2 TRUE 0.1 300 200 91.42 FALSE 0.1 300 200 97.28 TRUE 0.01 300 20093.38 FALSE 0.01 300 200 98.2 TRUE 0.001 300 200 93.3 FALSE 0.001 300200 98.08 TRUE 0.0001 300 200 92.68 FALSE 0.0001 300 200 98.12 TRUE0.00001 300 200 92.7 FALSE 0.00001 300 200 98.16 TRUE 0.1 300 300 90.2FALSE 0.1 300 300 97.1 TRUE 0.01 300 300 92.96 FALSE 0.01 300 300 98.16TRUE 0.001 300 300 93.64 FALSE 0.001 300 300 98.14 TRUE 0.0001 300 30092.92 FALSE 0.0001 300 300 98.18 TRUE 0.00001 300 300 92.54 FALSE0.00001 300 300 98.14

Similarly, “false positive” binding outcomes manifest as affinityreagent binding measurements occurring more frequently than expected.The tolerance to “false positive” binding outcomes was assessed byswitching a subset of binding outcomes from non-binding outcomes tobinding outcomes. The results of this assessment are provided in Table3.

TABLE 3 False Number of Positive Number of Probes Censored Rate ProbesImpacted Sensitivity TRUE 0.1 300 0 93.32 FALSE 0.1 300 0 98.04 TRUE 0.1300 1 92.54 FALSE 0.1 300 1 98.26 TRUE 0.01 300 1 92.74 FALSE 0.01 300 197.94 TRUE 0.001 300 1 92.48 FALSE 0.001 300 1 97.88 TRUE 0.0001 300 192.78 FALSE 0.0001 300 1 98.26 TRUE 0.00001 300 1 93.06 FALSE 0.00001300 1 98.16 TRUE 0.1 300 50 68.2 FALSE 0.1 300 50 89.32 TRUE 0.01 300 5091.28 FALSE 0.01 300 50 97.48 TRUE 0.001 300 50 92.66 FALSE 0.001 300 5098.1 TRUE 0.0001 300 50 93 FALSE 0.0001 300 50 98.16 TRUE 0.00001 300 5093.46 FALSE 0.00001 300 50 97.68 TRUE 0.1 300 100 40.98 FALSE 0.1 300100 75.02 TRUE 0.01 300 100 88.56 FALSE 0.01 300 100 96.94 TRUE 0.001300 100 93.34 FALSE 0.001 300 100 98.26 TRUE 0.0001 300 100 93.4 FALSE0.0001 300 100 97.96 TRUE 0.00001 300 100 92.62 FALSE 0.00001 300 10098.34 TRUE 0.1 300 200 14.8 FALSE 0.1 300 200 39.7 TRUE 0.01 300 20084.56 FALSE 0.01 300 200 95.58 TRUE 0.001 300 200 92.22 FALSE 0.001 300200 97.64 TRUE 0.0001 300 200 93.2 FALSE 0.0001 300 200 98.12 TRUE0.00001 300 200 92.08 FALSE 0.00001 300 200 98.16 TRUE 0.1 300 300 3.46FALSE 0.1 300 300 17.44 TRUE 0.01 300 300 79.46 FALSE 0.01 300 300 93.78TRUE 0.001 300 300 92.52 FALSE 0.001 300 300 97.94 TRUE 0.0001 300 30093.36 FALSE 0.0001 300 300 98.28 TRUE 0.00001 300 300 93.16 FALSE0.00001 300 300 97.78

These results, which are plotted in FIG. 12, indicate that theperformance of a censored protein identification approach degrades morerapidly than the uncensored protein identification approach withincreasing incidence of random false positive measurements. However,both approaches tolerate a false positive rate of 1 in 1000 in everyaffinity reagent cycle or a 1 in 100 rate in a subset of the affinityreagent cycles.

Example 13: Performance of Protein Inference with Overestimated orUnderestimated Affinity Reagent Binding Probabilities

Protein identification sensitivity was assessed using proteinidentification with correctly estimated affinity reagent to trimerbinding probabilities, and with overestimated or underestimated affinityreagent binding probabilities. The true binding probability was 0.25.The underestimated binding probabilities were: 0.05, 0.1, and 0.2. Theoverestimated binding probabilities were 0.30, 0.50, 0.75, and 0.90. Intotal, 300 cycles of affinity reagent measurements were acquired. None(0), all 300, or a subset (1, 50, 100, 200) of the affinity reagents hadthe overestimated or underestimated binding probabilities applied. Allothers had the correct binding probabilities (0.25) used in proteinidentification. The results of the analysis are provided in Table 4.

TABLE 4 Inference Number of Binding Number of Probes Sensi- True BindingCensored Probability Probes Impacted tivity Probability TRUE 0.05 300 093.32 0.25 FALSE 0.05 300 0 98.04 0.25 TRUE 0.05 300 1 94.04 0.25 FALSE0.05 300 1 98.6 0.25 TRUE 0.1 300 1 93.22 0.25 FALSE 0.1 300 1 97.8 0.25TRUE 0.2 300 1 92.64 0.25 FALSE 0.2 300 1 98.14 0.25 TRUE 0.25 300 193.24 0.25 FALSE 0.25 300 1 97.86 0.25 TRUE 0.3 300 1 93.3 0.25 FALSE0.3 300 1 98.24 0.25 TRUE 0.5 300 1 93.28 0.25 FALSE 0.5 300 1 97.960.25 TRUE 0.75 300 1 93.38 0.25 FALSE 0.75 300 1 97.94 0.25 TRUE 0.9 3001 92.84 0.25 FALSE 0.9 300 1 97.32 0.25 TRUE 0.05 300 50 92.22 0.25FALSE 0.05 300 50 97.8 0.25 TRUE 0.1 300 50 93.14 0.25 FALSE 0.1 300 5098.36 0.25 TRUE 0.2 300 50 93.5 0.25 FALSE 0.2 300 50 98.46 0.25 TRUE0.25 300 50 92.98 0.25 FALSE 0.25 300 50 98.16 0.25 TRUE 0.3 300 5092.42 0.25 FALSE 0.3 300 50 98.28 0.25 TRUE 0.5 300 50 93.18 0.25 FALSE0.5 300 50 98.18 0.25 TRUE 0.75 300 50 92.98 0.25 FALSE 0.75 300 50 96.90.25 TRUE 0.9 300 50 92.6 0.25 FALSE 0.9 300 50 94.18 0.25 TRUE 0.05 300100 92.7 0.25 FALSE 0.05 300 100 97.88 0.25 TRUE 0.1 300 100 93.14 0.25FALSE 0.1 300 100 97.94 0.25 TRUE 0.2 300 100 92.94 0.25 FALSE 0.2 300100 97.66 0.25 TRUE 0.25 300 100 92.74 0.25 FALSE 0.25 300 100 97.720.25 TRUE 0.3 300 100 93.06 0.25 FALSE 0.3 300 100 98.34 0.25 TRUE 0.5300 100 92.52 0.25 FALSE 0.5 300 100 98.2 0.25 TRUE 0.75 300 100 92.260.25 FALSE 0.75 300 100 95.88 0.25 TRUE 0.9 300 100 91.54 0.25 FALSE 0.9300 100 84.26 0.25 TRUE 0.05 300 200 91.6 0.25 FALSE 0.05 300 200 95.220.25 TRUE 0.1 300 200 93.36 0.25 FALSE 0.1 300 200 97.76 0.25 TRUE 0.2300 200 92.96 0.25 FALSE 0.2 300 200 97.88 0.25 TRUE 0.25 300 200 93.280.25 FALSE 0.25 300 200 98.28 0.25 TRUE 0.3 300 200 92.7 0.25 FALSE 0.3300 200 97.6 0.25 TRUE 0.5 300 200 92.36 0.25 FALSE 0.5 300 200 97.340.25 TRUE 0.75 300 200 91.22 0.25 FALSE 0.75 300 200 88.52 0.25 TRUE 0.9300 200 90.52 0.25 FALSE 0.9 300 200 33 0.25 TRUE 0.05 300 300 91.7 0.25FALSE 0.05 300 300 0 0.25 TRUE 0.1 300 300 92.66 0.25 FALSE 0.1 300 30092.06 0.25 TRUE 0.2 300 300 92.78 0.25 FALSE 0.2 300 300 98.02 0.25 TRUE0.25 300 300 93.56 0.25 FALSE 0.25 300 300 98.02 0.25 TRUE 0.3 300 30093 0.25 FALSE 0.3 300 300 98.22 0.25 TRUE 0.5 300 300 91.6 0.25 FALSE0.5 300 300 96.72 0.25 TRUE 0.75 300 300 90.36 0.25 FALSE 0.75 300 30067.08 0.25 TRUE 0.9 300 300 88.72 0.25 FALSE 0.9 300 300 0.58 0.25

These results, which are plotted in FIG. 13, show that censored proteinidentification may be a preferred approach in some cases where bindingprobabilities may not be accurately estimated.

Example 14: Performance of Protein Inference Approaches Using AffinityReagents with Unknown Binding Epitopes

In some cases, affinity reagents may possess a number of binding sites(e.g., epitopes) which are unknown. The sensitivity of censored proteinidentification and uncensored protein identification approaches withaffinity reagent binding measurements were compared using affinityreagents that each bind five trimer sites (e.g. a targeted trimer, andfour random off-target sites) with probability 0.25 that are input intothe protein identification algorithm. A subset of the affinity reagents(0 of 300, 1 of 300, 50 of 300, 100 of 300, 200 of 300, or 300 of 300)had either 1, 4, or 40 additional extra binding sites each against arandom trimer with binding probability 0.05, 0.1 or 0.25. The results ofthe analysis are shown in Table 5.

TABLE 5 Extra Sites Number of Number of Binding Number of Probes UnknownCensored Probability Probes Impacted Sensitivity Extra Sites TRUE 0.05300 0 93.32 1 FALSE 0.05 300 0 98.04 1 TRUE 0.05 300 1 93.14 1 FALSE0.05 300 1 97.96 1 TRUE 0.05 300 1 92.68 4 FALSE 0.05 300 1 98.12 4 TRUE0.05 300 1 92.32 40 FALSE 0.05 300 1 97.82 40 TRUE 0.1 300 1 92.28 1FALSE 0.1 300 1 98.02 1 TRUE 0.1 300 1 92.56 4 FALSE 0.1 300 1 98.34 4TRUE 0.1 300 1 92.64 40 FALSE 0.1 300 1 97.86 40 TRUE 0.25 300 1 93.42 1FALSE 0.25 300 1 98.46 1 TRUE 0.25 300 1 92.94 4 FALSE 0.25 300 1 98.124 TRUE 0.25 300 1 92.36 40 FALSE 0.25 300 1 98.1 40 TRUE 0.05 300 5093.16 1 FALSE 0.05 300 50 97.94 1 TRUE 0.05 300 50 92.12 4 FALSE 0.05300 50 97.44 4 TRUE 0.05 300 50 67.5 40 FALSE 0.05 300 50 96.26 40 TRUE0.1 300 50 92.92 1 FALSE 0.1 300 50 98.34 1 TRUE 0.1 300 50 90.64 4FALSE 0.1 300 50 97.88 4 TRUE 0.1 300 50 34.98 40 FALSE 0.1 300 50 92.2440 TRUE 0.25 300 50 91.52 1 FALSE 0.25 300 50 98.12 1 TRUE 0.25 300 5083.52 4 FALSE 0.25 300 50 97 4 TRUE 0.25 300 50 2.92 40 FALSE 0.25 30050 37.52 40 TRUE 0.05 300 100 93 1 FALSE 0.05 300 100 97.84 1 TRUE 0.05300 100 90.3 4 FALSE 0.05 300 100 97.56 4 TRUE 0.05 300 100 28.88 40FALSE 0.05 300 100 90.12 40 TRUE 0.1 300 100 90.86 1 FALSE 0.1 300 10097.96 1 TRUE 0.1 300 100 88.52 4 FALSE 0.1 300 100 97.9 4 TRUE 0.1 300100 3.14 40 FALSE 0.1 300 100 35.04 40 TRUE 0.25 300 100 88.4 1 FALSE0.25 300 100 97.68 1 TRUE 0.25 300 100 70.06 4 FALSE 0.25 300 100 95.264 TRUE 0.25 300 100 0.24 40 FALSE 0.25 300 100 0.08 40 TRUE 0.05 300 20091.68 1 FALSE 0.05 300 200 98.22 1 TRUE 0.05 300 200 86.8 4 FALSE 0.05300 200 98.1 4 TRUE 0.05 300 200 2.14 40 FALSE 0.05 300 200 26.82 40TRUE 0.1 300 200 89.18 1 FALSE 0.1 300 200 97.96 1 TRUE 0.1 300 20075.24 4 FALSE 0.1 300 200 96.36 4 TRUE 0.1 300 200 0.16 40 FALSE 0.1 300200 0.16 40 TRUE 0.25 300 200 84.8 1 FALSE 0.25 300 200 96.7 1 TRUE 0.25300 200 30.92 4 FALSE 0.25 300 200 90.92 4 TRUE 0.25 300 200 0.02 40FALSE 0.25 300 200 0 40 TRUE 0.05 300 300 91.72 1 FALSE 0.05 300 30097.68 1 TRUE 0.05 300 300 79.84 4 FALSE 0.05 300 300 96.88 4 TRUE 0.05300 300 0.64 40 FALSE 0.05 300 300 1.26 40 TRUE 0.1 300 300 88.3 1 FALSE0.1 300 300 98.34 1 TRUE 0.1 300 300 54.92 4 FALSE 0.1 300 300 95.32 4TRUE 0.1 300 300 0 40 FALSE 0.1 300 300 0 40 TRUE 0.25 300 300 74.6 1FALSE 0.25 300 300 97.26 1 TRUE 0.25 300 300 6.22 4 FALSE 0.25 300 30058.24 4 TRUE 0.25 300 300 0 40 FALSE 0.25 300 300 0 40

These results, which are plotted in FIG. 14, show that uncensoredinference is more tolerant to the inclusion of additional hidden bindingsites, and that the performance of both inference approaches issignificantly compromised when 50 of the 300 affinity reagents contain40 additional binding sites.

Example 15: Performance of Protein Inference Approaches Using AffinityReagents with Missing Binding Epitopes

In some cases, there may be improperly characterized affinity reagentswith a number of annotated binding epitopes that do not exist (e.g.,extra expected binding sites). That is, the model used to generateexpected binding probabilities for an affinity reagent contains extraexpected sites that do not exist. The sensitivity of censored proteinidentification and uncensored protein identification approaches withaffinity reagent binding measurements were compared using affinityreagents that each bind random trimer sites (e.g. a targeted trimer, andfour random off-target sites) with probability 0.25 that are input intothe protein identification algorithm. A subset of the affinity reagents(0 of 300, 1 of 300, 50 of 300, 100 of 300, 200 of 300, or 300 of 300)had either 1, 4, or 40 extra expected binding sites each against arandom trimer with binding probability 0.05, 0.1 or 0.25 added to themodel for the affinity reagent used by the protein inference algorithm.The results of the analysis are shown in Table 6.

TABLE 6 Extra Sites Number of Binding Number of Number of ProbesCensored Probability Extra Sites Probes Impacted Sensitivity TRUE 0.05 1300 0 93.32 FALSE 0.05 1 300 0 98.04 TRUE 0.05 1 300 1 94.06 FALSE 0.051 300 1 98.6 TRUE 0.05 4 300 1 93.08 FALSE 0.05 4 300 1 98.6 TRUE 0.0540 300 1 93.38 FALSE 0.05 40 300 1 98.1 TRUE 0.1 1 300 1 92.98 FALSE 0.11 300 1 97.88 TRUE 0.1 4 300 1 93.54 FALSE 0.1 4 300 1 98.2 TRUE 0.1 40300 1 93.26 FALSE 0.1 40 300 1 98.12 TRUE 0.25 1 300 1 92.98 FALSE 0.251 300 1 97.62 TRUE 0.25 4 300 1 92.7 FALSE 0.25 4 300 1 98.16 TRUE 0.2540 300 1 93.06 FALSE 0.25 40 300 1 97.66 TRUE 0.05 1 300 50 92.4 FALSE0.05 1 300 50 98.2 TRUE 0.05 4 300 50 92.66 FALSE 0.05 4 300 50 98.1TRUE 0.05 40 300 50 91.14 FALSE 0.05 40 300 50 97.66 TRUE 0.1 1 300 5093.22 FALSE 0.1 1 300 50 97.9 TRUE 0.1 4 300 50 92.04 FALSE 0.1 4 300 5097.56 TRUE 0.1 40 300 50 87.74 FALSE 0.1 40 300 50 97.08 TRUE 0.25 1 30050 92.28 FALSE 0.25 1 300 50 98.26 TRUE 0.25 4 300 50 91.8 FALSE 0.25 4300 50 97.62 TRUE 0.25 40 300 50 87.16 FALSE 0.25 40 300 50 93.52 TRUE0.05 1 300 100 91.9 FALSE 0.05 1 300 100 97.64 TRUE 0.05 4 300 100 92.74FALSE 0.05 4 300 100 98.02 TRUE 0.05 40 300 100 84.18 FALSE 0.05 40 300100 97.42 TRUE 0.1 1 300 100 92.82 FALSE 0.1 1 300 100 98.08 TRUE 0.1 4300 100 92.46 FALSE 0.1 4 300 100 97.82 TRUE 0.1 40 300 100 76.28 FALSE0.1 40 300 100 95.2 TRUE 0.25 1 300 100 91.18 FALSE 0.25 1 300 100 97.84TRUE 0.25 4 300 100 90.38 FALSE 0.25 4 300 100 97.64 TRUE 0.25 40 300100 60.5 FALSE 0.25 40 300 100 46.34 TRUE 0.05 1 300 200 93.32 FALSE0.05 1 300 200 98.16 TRUE 0.05 4 300 200 90.42 FALSE 0.05 4 300 20097.68 TRUE 0.05 40 300 200 74.82 FALSE 0.05 40 300 200 92.86 TRUE 0.1 1300 200 93.28 FALSE 0.1 1 300 200 98.2 TRUE 0.1 4 300 200 90.62 FALSE0.1 4 300 200 98.04 TRUE 0.1 40 300 200 55.4 FALSE 0.1 40 300 200 46.62TRUE 0.25 1 300 200 92.14 FALSE 0.25 1 300 200 97.88 TRUE 0.25 4 300 20085.22 FALSE 0.25 4 300 200 96.68 TRUE 0.25 40 300 200 4.92 FALSE 0.25 40300 200 0.34 TRUE 0.05 1 300 300 92.8 FALSE 0.05 1 300 300 98.34 TRUE0.05 4 300 300 91.04 FALSE 0.05 4 300 300 97.9 TRUE 0.05 40 300 300 53.2FALSE 0.05 40 300 300 54.84 TRUE 0.1 1 300 300 91.28 FALSE 0.1 1 300 30097.44 TRUE 0.1 4 300 300 85.08 FALSE 0.1 4 300 300 97.08 TRUE 0.1 40 300300 10.66 FALSE 0.1 40 300 300 1.76 TRUE 0.25 1 300 300 90.64 FALSE 0.251 300 300 97.54 TRUE 0.25 4 300 300 78.6 FALSE 0.25 4 300 300 95.36 TRUE0.25 40 300 300 0.06 FALSE 0.25 40 300 300 0

These results, which are plotted in FIG. 15, show that uncensoredinference is more tolerant to the inclusion of extra expected bindingsites included in the model of affinity reagent binding, and that theperformance of both protein identification approaches is compromised tosome degree when the majority of affinity reagents contain 40 extraexpected binding sites.

Example 16: Censored Inference for Affinity Reagent Binding Analysiswith an Alternative Scaling Strategy

The methods described herein may be applied to infer protein identity(e.g., identify unknown proteins) using affinity reagent bindingmeasurements in combination with various probability scaling strategies.The censored inference approach described in Example 11 scales theprobability of an observed outcome for a protein based on the number ofpotential binding sites on the protein (protein length—2) and the numberof observed binding outcomes (M):

${SL}_{Protein} = \frac{P\left( {{outcome}\mspace{14mu}{set}} \middle| {protein} \right)}{\begin{pmatrix}{L - 2} \\M\end{pmatrix}}$

The methods described herein may be applied with alternative approachesfor computing scaled likelihoods. This example applies an alternativeapproach for normalization that models the probability of generating Nbinding events for a protein of length k from the set of affinityreagents used to measure the protein, and scales based on thisprobability. First, for each probe, the probability of the probe bindinga trimer of unknown identity in the sample is calculated:

${P\left( {{trimer}\mspace{14mu}{bind}} \middle| {probe}_{i} \right)} = {\sum\limits_{j = 1}^{j = 8000}{{P\left( {trimer}_{j} \right)}{P\left( {{probe}_{i}\mspace{14mu}{bind}} \middle| {trimer}_{j} \right)}}}$where P(trimer_(j)) is the frequency with which the trimer occursrelative to the summed count of all 8,000 trimers in the proteome. Forany protein of length k, the probability of a probe i binding theprotein may be given by:P(protein bind|probe_(i) ,k)=1−(1−P(trimer bind|probe_(i)))^(k−2)

The number of successful binding events observed for a protein of lengthk may follow a Poisson-Binomial distribution with n trials, where n isthe number of probe binding measurements made for the protein and theparameters p_(probes,k) of the distribution indicate the probability ofsuccess for each trial:p _(probes,k)=[P(bind|probe_(1,k)),P(bind|probe₂ ,k),P(bind|probe₃ ,k) .. . P(bind|probe_(n) ,k)].

The probability of generating N binding events from a protein of lengthk, with a particular set of probes, may be given by the probability massfunction of the Poisson binomial distribution (PMF_(PoiBin))parameterized by p, evaluated at N:P(N binding events|probes,k)=PMF _(PoiBin)(N,p _(probes,k))

The scaled likelihood of a particular outcome set is computed based onthis probability:

${SL}_{{protein},{{binding}\mspace{14mu}{events}}} = \frac{P\left( {{outcome}\mspace{14mu}{set}} \middle| {protein} \right)}{P\left( {\left. {N\mspace{14mu}{binding}\mspace{14mu}{events}} \middle| {probes} \right.,k} \right)}$

Example 17: Using Randomly Selected Affinity Reagents

The methods described herein may be applied to any set of affinityreagents. For example, the protein identification approach may beapplied to a set of affinity reagents targeting the most abundanttrimers in the proteome, or targeting random trimers. The results from ahuman protein inference analysis using affinity reagents targeting thetop 300 least abundant trimers in the proteome, 300 randomly selectedtrimers in the proteome, or the 300 most abundant trimers in theproteome, are shown in Tables 7A-7C, respectively.

Tables 7A-C

TABLE 7A 300 affinity reagents targeting the least- abundant trimers inthe proteome Number of Probe Set Experiment Selection Probes IDRepetition Type Sensitivity 300 100 0 Bottom 300 91.9 300 100 1 Bottom300 91.24 300 100 2 Bottom 300 91.74 300 100 3 Bottom 300 90.9 300 100 4Bottom 300 90.46

TABLE 7B 300 affinity reagents targeting random trimers in the proteomeNumber of Probe Set Experiment Selection Probes ID Repetition TypeSensitivity 300 0 0 Random 94.4 300 0 1 Random 94.2 300 0 2 Random 94.18300 0 3 Random 94.64 300 0 4 Random 94.24 300 1 0 Random 94.12 300 1 1Random 94.08 300 1 2 Random 94.12 300 1 3 Random 93.7 300 1 4 Random93.54 300 2 0 Random 93.68 300 2 1 Random 93.68 300 2 2 Random 93.68 3002 3 Random 93.74 300 2 4 Random 93.9 300 3 0 Random 95.12 300 3 1 Random94.38 300 3 2 Random 94.76 300 3 3 Random 95.4 300 3 4 Random 94.6 300 40 Random 94.46 300 4 1 Random 94.74 300 4 2 Random 95.04 300 4 3 Random94.66 300 4 4 Random 94.76 300 5 0 Random 94.58 300 5 1 Random 94.62 3005 2 Random 94.48 300 5 3 Random 94.48 300 5 4 Random 95 300 6 0 Random93.18 300 6 1 Random 93.44 300 6 2 Random 93.28 300 6 3 Random 93.8 3006 4 Random 94.26 300 7 0 Random 95.16 300 7 1 Random 94.02 300 7 2Random 95 300 7 3 Random 95.1 300 7 4 Random 94.86 300 8 0 Random 93.56300 8 1 Random 95.5 300 8 2 Random 94.7 300 8 3 Random 94.72 300 8 4Random 94.94 300 9 0 Random 94.46 300 9 1 Random 95.44 300 9 2 Random93.98 300 9 3 Random 94.58 300 9 4 Random 94.34 300 10 0 Random 94.54300 10 1 Random 94.56 300 10 2 Random 94.78 300 10 3 Random 94.86 300 104 Random 95.08 300 11 0 Random 94.36 300 11 1 Random 94.86 300 11 2Random 95.3 300 11 3 Random 94.16 300 11 4 Random 94.9 300 12 0 Random94.92 300 12 1 Random 94.66 300 12 2 Random 94.26 300 12 3 Random 94.58300 12 4 Random 94.02 300 13 0 Random 94.78 300 13 1 Random 94.54 300 132 Random 95.02 300 13 3 Random 94.94 300 13 4 Random 94.98 300 14 0Random 95.3 300 14 1 Random 94.36 300 14 2 Random 94.76 300 14 3 Random95.26 300 14 4 Random 94.52 300 15 0 Random 94.48 300 15 1 Random 94.6300 15 2 Random 94.98 300 15 3 Random 94.6 300 15 4 Random 95.8 300 16 0Random 94.58 300 16 1 Random 92.96 300 16 2 Random 94.6 300 16 3 Random93.84 300 16 4 Random 94.38 300 17 0 Random 94.76 300 17 1 Random 94.54300 17 2 Random 94.72 300 17 3 Random 94.24 300 17 4 Random 94.12 300 180 Random 94.16 300 18 1 Random 94.1 300 18 2 Random 94.86 300 18 3Random 93.98 300 18 4 Random 95.04 300 19 0 Random 93.58 300 19 1 Random94.94 300 19 2 Random 95.12 300 19 3 Random 94.8 300 19 4 Random 94.8300 20 0 Random 93 300 20 1 Random 94.22 300 20 2 Random 94.4 300 20 3Random 93.64 300 20 4 Random 94.76 300 21 0 Random 93.68 300 21 1 Random94.18 300 21 2 Random 94.38 300 21 3 Random 94.48 300 21 4 Random 94.68300 22 0 Random 93.66 300 22 1 Random 94.16 300 22 2 Random 94.1 300 223 Random 94.16 300 22 4 Random 94.1 300 23 0 Random 93.94 300 23 1Random 94.42 300 23 2 Random 94.24 300 23 3 Random 93.9 300 23 4 Random94.4 300 24 0 Random 95 300 24 1 Random 94.82 300 24 2 Random 94.16 30024 3 Random 94.58 300 24 4 Random 94.54 300 25 0 Random 94.5 300 25 1Random 95.1 300 25 2 Random 95.3 300 25 3 Random 94.54 300 25 4 Random95.22 300 26 0 Random 94.22 300 26 1 Random 94.08 300 26 2 Random 94.52300 26 3 Random 94.3 300 26 4 Random 94.6 300 27 0 Random 93.92 300 27 1Random 94.24 300 27 2 Random 93.64 300 27 3 Random 93.84 300 27 4 Random94.04 300 28 0 Random 94.08 300 28 1 Random 95.14 300 28 2 Random 94.82300 28 3 Random 94.7 300 28 4 Random 94.92 300 29 0 Random 94.82 300 291 Random 93.76 300 29 2 Random 93.98 300 29 3 Random 93.14 300 29 4Random 94.46 300 30 0 Random 94.6 300 30 1 Random 96.22 300 30 2 Random95.06 300 30 3 Random 95.12 300 30 4 Random 94.82 300 31 0 Random 93.12300 31 1 Random 93.92 300 31 2 Random 93.3 300 31 3 Random 94.7 300 31 4Random 94.22 300 32 0 Random 93.7 300 32 1 Random 94.62 300 32 2 Random94.12 300 32 3 Random 94.08 300 32 4 Random 94.72 300 33 0 Random 94.82300 33 1 Random 93.44 300 33 2 Random 94.06 300 33 3 Random 94.54 300 334 Random 94.42 300 34 0 Random 94.16 300 34 1 Random 93.28 300 34 2Random 94.9 300 34 3 Random 93.12 300 34 4 Random 94.3 300 35 0 Random94.54 300 35 1 Random 93.56 300 35 2 Random 93.4 300 35 3 Random 93.78300 35 4 Random 94.5 300 36 0 Random 94.34 300 36 1 Random 93.9 300 36 2Random 94.7 300 36 3 Random 95.12 300 36 4 Random 94.8 300 37 0 Random94.38 300 37 1 Random 95.22 300 37 2 Random 94.98 300 37 3 Random 94.12300 37 4 Random 95.06 300 38 0 Random 94.34 300 38 1 Random 94.82 300 382 Random 93.8 300 38 3 Random 94.8 300 38 4 Random 95.1 300 39 0 Random93.72 300 39 1 Random 93.7 300 39 2 Random 94.12 300 39 3 Random 94.04300 39 4 Random 93.98 300 40 0 Random 94.42 300 40 1 Random 93.86 300 402 Random 93.46 300 40 3 Random 94.34 300 40 4 Random 94.12 300 41 0Random 94.16 300 41 1 Random 95 300 41 2 Random 95.22 300 41 3 Random95.38 300 41 4 Random 95.36 300 42 0 Random 93.36 300 42 1 Random 94.38300 42 2 Random 94.28 300 42 3 Random 94.52 300 42 4 Random 93.94 300 430 Random 95.5 300 43 1 Random 95.04 300 43 2 Random 95.32 300 43 3Random 94.84 300 43 4 Random 95.26 300 44 0 Random 94.74 300 44 1 Random94.6 300 44 2 Random 93.8 300 44 3 Random 94.04 300 44 4 Random 94.22300 45 0 Random 93.64 300 45 1 Random 93.78 300 45 2 Random 94.12 300 453 Random 94.48 300 45 4 Random 94.66 300 46 0 Random 94.48 300 46 1Random 94.92 300 46 2 Random 95.04 300 46 3 Random 94.14 300 46 4 Random94.6 300 47 0 Random 94.2 300 47 1 Random 93.56 300 47 2 Random 95.36300 47 3 Random 95.64 300 47 4 Random 94.18 300 48 0 Random 94.38 300 481 Random 95.1 300 48 2 Random 94.24 300 48 3 Random 94.6 300 48 4 Random94.76 300 49 0 Random 94.98 300 49 1 Random 95.9 300 49 2 Random 95.08300 49 3 Random 94.72 300 49 4 Random 94.02 300 50 0 Random 94.72 300 501 Random 94.44 300 50 2 Random 95.84 300 50 3 Random 95 300 50 4 Random94.62 300 51 0 Random 94.92 300 51 1 Random 94.26 300 51 2 Random 94.34300 51 3 Random 94.66 300 51 4 Random 93.58 300 52 0 Random 94.98 300 521 Random 95.12 300 52 2 Random 94.88 300 52 3 Random 94.78 300 52 4Random 94.88 300 53 0 Random 94.88 300 53 1 Random 95.04 300 53 2 Random94.18 300 53 3 Random 94.04 300 53 4 Random 94.56 300 54 0 Random 94.26300 54 1 Random 94.1 300 54 2 Random 95.32 300 54 3 Random 94.44 300 544 Random 94.74 300 55 0 Random 94.68 300 55 1 Random 94.68 300 55 2Random 95.52 300 55 3 Random 94.54 300 55 4 Random 95.12 300 56 0 Random94.58 300 56 1 Random 95.14 300 56 2 Random 94.58 300 56 3 Random 95.18300 56 4 Random 94.84 300 57 0 Random 94.54 300 57 1 Random 93.82 300 572 Random 94.92 300 57 3 Random 95.14 300 57 4 Random 94.26 300 58 0Random 94.36 300 58 1 Random 94.74 300 58 2 Random 94.92 300 58 3 Random94.36 300 58 4 Random 94.28 300 59 0 Random 94.54 300 59 1 Random 93.92300 59 2 Random 95.04 300 59 3 Random 95.4 300 59 4 Random 93.76 300 600 Random 94.8 300 60 1 Random 94.74 300 60 2 Random 93.82 300 60 3Random 94.54 300 60 4 Random 93.86 300 61 0 Random 94.5 300 61 1 Random94.76 300 61 2 Random 94.3 300 61 3 Random 94.68 300 61 4 Random 94.42300 62 0 Random 93.72 300 62 1 Random 94.94 300 62 2 Random 94.12 300 623 Random 93.86 300 62 4 Random 95.38 300 63 0 Random 95.1 300 63 1Random 95.4 300 63 2 Random 94.94 300 63 3 Random 94.62 300 63 4 Random94.32 300 64 0 Random 94.96 300 64 1 Random 94.02 300 64 2 Random 94.52300 64 3 Random 93.98 300 64 4 Random 94.48 300 65 0 Random 93.6 300 651 Random 94.4 300 65 2 Random 93.38 300 65 3 Random 94.54 300 65 4Random 93.14 300 66 0 Random 94.44 300 66 1 Random 94.2 300 66 2 Random94.9 300 66 3 Random 94.68 300 66 4 Random 94.6 300 67 0 Random 94.3 30067 1 Random 94.08 300 67 2 Random 94.56 300 67 3 Random 93.78 300 67 4Random 94.52 300 68 0 Random 93.24 300 68 1 Random 93.76 300 68 2 Random94.8 300 68 3 Random 94.36 300 68 4 Random 93.76 300 69 0 Random 94.58300 69 1 Random 94.52 300 69 2 Random 94.72 300 69 3 Random 94.88 300 694 Random 93.38 300 70 0 Random 95.34 300 70 1 Random 94.52 300 70 2Random 94.38 300 70 3 Random 94.94 300 70 4 Random 93.6 300 71 0 Random93.8 300 71 1 Random 94.38 300 71 2 Random 94.32 300 71 3 Random 93.2300 71 4 Random 94.28 300 72 0 Random 94.76 300 72 1 Random 95 300 72 2Random 95.64 300 72 3 Random 95.28 300 72 4 Random 95.68 300 73 0 Random94.92 300 73 1 Random 94.52 300 73 2 Random 94.36 300 73 3 Random 94.38300 73 4 Random 94.56 300 74 0 Random 94.62 300 74 1 Random 94.18 300 742 Random 94.38 300 74 3 Random 94.38 300 74 4 Random 93.5 300 75 0Random 95.32 300 75 1 Random 95.42 300 75 2 Random 94.9 300 75 3 Random94.96 300 75 4 Random 94.1 300 76 0 Random 94.9 300 76 1 Random 95.46300 76 2 Random 94.72 300 76 3 Random 94.54 300 76 4 Random 94.16 300 770 Random 94.14 300 77 1 Random 93.94 300 77 2 Random 94.28 300 77 3Random 94.62 300 77 4 Random 94.38 300 78 0 Random 93.8 300 78 1 Random93.84 300 78 2 Random 94.56 300 78 3 Random 94.18 300 78 4 Random 93.76300 79 0 Random 94.28 300 79 1 Random 93.66 300 79 2 Random 93.76 300 793 Random 94.6 300 79 4 Random 95.76 300 80 0 Random 94.52 300 80 1Random 94.82 300 80 2 Random 93.82 300 80 3 Random 94.9 300 80 4 Random94.3 300 81 0 Random 94.84 300 81 1 Random 94.82 300 81 2 Random 94.76300 81 3 Random 94.54 300 81 4 Random 94.74 300 82 0 Random 95.26 300 821 Random 94.32 300 82 2 Random 94.04 300 82 3 Random 94.98 300 82 4Random 94.56 300 83 0 Random 94.9 300 83 1 Random 94.76 300 83 2 Random94.06 300 83 3 Random 94.46 300 83 4 Random 94.8 300 84 0 Random 93.66300 84 1 Random 93.28 300 84 2 Random 94.64 300 84 3 Random 93.58 300 844 Random 93.86 300 85 0 Random 94.16 300 85 1 Random 93.06 300 85 2Random 94.02 300 85 3 Random 93.1 300 85 4 Random 94.3 300 86 0 Random94.18 300 86 1 Random 95.02 300 86 2 Random 93.9 300 86 3 Random 94.58300 86 4 Random 94.8 300 87 0 Random 95.18 300 87 1 Random 95.52 300 872 Random 95.38 300 87 3 Random 95.7 300 87 4 Random 94.72 300 88 0Random 94.52 300 88 1 Random 93.7 300 88 2 Random 94.36 300 88 3 Random94.14 300 88 4 Random 95.1 300 89 0 Random 93.62 300 89 1 Random 94.8300 89 2 Random 94.1 300 89 3 Random 94.96 300 89 4 Random 94.68 300 900 Random 94.6 300 90 1 Random 94.04 300 90 2 Random 94.14 300 90 3Random 94.36 300 90 4 Random 94.24 300 91 0 Random 94.12 300 91 1 Random94.32 300 91 2 Random 93.7 300 91 3 Random 94.56 300 91 4 Random 94.68300 92 0 Random 95.06 300 92 1 Random 94.06 300 92 2 Random 95.48 300 923 Random 95.48 300 92 4 Random 95.24 300 93 0 Random 93.46 300 93 1Random 94.4 300 93 2 Random 93.62 300 93 3 Random 94.72 300 93 4 Random95.16 300 94 0 Random 95 300 94 1 Random 94.74 300 94 2 Random 94.1 30094 3 Random 94.26 300 94 4 Random 95.02 300 95 0 Random 94.94 300 95 1Random 94.6 300 95 2 Random 93.9 300 95 3 Random 95.16 300 95 4 Random94.14 300 96 0 Random 95.08 300 96 1 Random 94.54 300 96 2 Random 94.6300 96 3 Random 95.14 300 96 4 Random 93.88 300 97 0 Random 93.66 300 971 Random 94.32 300 97 2 Random 93.76 300 97 3 Random 94.1 300 97 4Random 93.64 300 98 0 Random 95.48 300 98 1 Random 94.34 300 98 2 Random94.96 300 98 3 Random 94.74 300 98 4 Random 95.28 300 99 0 Random 93.86300 99 1 Random 94.2 300 99 2 Random 94.98 300 99 3 Random 94.38 300 994 Random 94.44

TABLE 7C 300 affinity reagents targeting the most-abundant trimers inthe proteome Number of Probe Set Experiment Selection Probes IDRepetitions Type Sensitivity 300 101 0 Top 300 97.98 300 101 1 Top 30097.24 300 101 2 Top 300 97.94 300 101 3 Top 300 98.18 300 101 4 Top 30097.12

These results are plotted in FIG. 16. In all cases, each affinityreagent had a binding probability of 0.25 to the targeted trimer, and abinding probability of 0.25 to 4 additional randomly selected trimers.The performance of each affinity reagent set is measured based onsensitivity (e.g., the percentage of proteins identified). Each affinityreagent set was assessed in 5 replicates, with the performance of eachreplicate plotted as a dot, and a vertical line connecting replicatemeasurements from the same set of affinity reagents. The results fromthe affinity reagent set consisting of the top 300 most abundantaffinity reagents is in blue, the bottom 300 in green. A total of 100different sets of 300 affinity reagents targeting random trimers weregenerated and assessed. Each of those sets is represented by a set of 5grey points (one for each replicate) connected by a vertical grey line.According to the uncensored inference used in this analysis, targetingmore abundant trimers improves identification performance as compared totargeting random trimers.

Example 18: Affinity Reagents with Biosimilar Off-Target Sites

The methods described herein may be applied to affinity reagent bindingexperiment with affinity reagents having different types of off-targetbinding sites (epitopes). In this example, performance with two classesof affinity reagents are compared: random, and “biosimilar” affinityreagents. The results from these assessments are shown in Tables 8A-8D.

Tables 8A-D

TABLE 8A Performance of Censored Inference with Affinity Reagents havingBiosimilar Off- Target Sites and Targeting the 300 Most-Abundant Trimersin the Proteome Number of Censored Cycles Probe Type Sensitivity TRUE100 Biosimilar 0.00634 TRUE 200 Biosimilar 31.97667 TRUE 300 Biosimilar68.73336

TABLE 8B Performance of Uncensored Inference with Affinity Reagentshaving Biosimilar Off-Target Sites and Targeting the 300 Most-AbundantTrimers in the Proteome Number of Censored Cycles Probe Type SensitivityFALSE 100 Biosimilar 75.67516 FALSE 200 Biosimilar 97.68607 FALSE 300Biosimilar 99.06809

TABLE 8C Performance of Censored Inference with Affinity Reagents havingRandom Off-Target Sites and Targeting the 300 Most-Abundant Trimers inthe Proteome Number of Censored Cycles Probe Type Sensitivity TRUE 100Random 0.082414 TRUE 200 Random 74.68619 TRUE 300 Random 93.13427

TABLE 8D Performance of Uncensored Inference with Affinity Reagentshaving Random Off-Target Sites and Targeting the 300 Most-AbundantTrimers in the Proteome Number of Censored Cycles Probe Type SensitivityFALSE 100 Random 60.02916 FALSE 200 Random 95.47356 FALSE 300 Random98.51021

Unlike the random affinity reagents, the biosimilar affinity reagentshave off-target binding sites that are biochemically similar to thetargeted epitope. Both the random and biosimilar affinity reagentsrecognize their target epitope (e.g., a trimer) with binding probability0.25. Each of the random class of affinity reagents has 4 randomlyselected off-target trimer binding sites with binding probability 0.25.In contrast, the 4 off-target binding sites for the “biosimilar”affinity reagents are the four trimers most similar to the trimertargeted by the affinity reagent, which are bound with probability 0.25.For these biosimilar affinity reagents, the similarity between trimersequences is computed by summing the BLOSUM62 coefficient for the aminoacid pair at each sequence location. Both the random and biosimilaraffinity reagent sets target the top 300 most abundant trimers in thehuman proteome, where abundance is measured as the number of uniqueproteins containing one or more instances of the trimer. FIG. 17 showsthe performance of the censored (dashed lines) and uncensored (solidlines) protein inference approaches in terms of the percent of proteinsidentified in a human sample when affinity reagents with random (blue)or biosimilar (orange) off-target sites are used.

In this comparison, uncensored inference outperforms censored inference,with uncensored inference performing better in the case of biosimilaraffinity reagents, and censored inference performing better in the caseof random affinity reagents.

Alternatively, rather than using affinity reagents targeting the mostabundant trimers in the proteome, an optimal set of trimer targets maybe chosen for a particular approach based on the candidate proteins thatmay be measured (for example, the human proteome), the type of proteininference being performed (censored or uncensored), and the type ofaffinity reagents being used (random or biosimilar). A “greedy”algorithm, as described below, may be used to select a set of optimalaffinity reagents:

-   -   1) Initialize an empty list of selected affinity reagents (AR).    -   2) Initialize a set of candidate ARs (e.g., a collection of        8,000 ARs, each targeting a unique trimer with random off-target        sites).    -   3) Select a set of protein sequences to optimize against (e.g.,        all human proteins in the Uniprot reference proteome).    -   4) Repeat the following until the desired number of ARs has been        selected:        -   a. For each candidate AR:            -   i. Simulate binding of the candidate AR against the                protein set.            -   ii. Perform protein inference for each protein using the                simulated binding measurements from the candidate AR and                the simulated binding measurements from all previously                selected ARs.            -   iii. Calculate a score for the candidate AR by summing                up the probability of the correct protein identification                for each protein determined by protein inference.        -   b. Add the AR with the highest score to the set of selected            ARs, and remove it from the candidate AR list.

The greedy approach was used to select 300 optimal affinity reagentsfrom either the collection of random affinity reagents or biosimilaraffinity reagents targeting the top 4,000 most abundant trimers in thehuman proteome. The optimization was performed for both censored proteininference and uncensored protein inference. The results from theseoptimizations are provided in Tables 9A-9D.

Tables 9A-D

TABLE 9A Performance of Censored Inference with Affinity Reagents havingBiosimilar Off-Target Sites and Targeting the 300 Optimal Trimers in theProteome Number of Censored Cycles Probe Type Sensitivity TRUE 100Biosimilar 25.58007 TRUE 200 Biosimilar 87.82173 TRUE 300 Biosimilar95.15025

TABLE 9B Performance of Uncensored Inference with Affinity Reagentshaving Biosimilar Off-Target Sites and Targeting the 300 Optimal Trimersin the Proteome Number of Censored Cycles Probe Type Sensitivity FALSE100 Biosimilar 76.76556 FALSE 200 Biosimilar 97.2106 FALSE 300Biosimilar 99.03005

TABLE 9C Performance of Censored Inference with Affinity Reagents havingRandom Off-Target Sites and Targeting the 300 Optimal Trimers in theProteome Number of Censored Cycles Probe Type Sensitivity TRUE 100Random 24.93343 TRUE 200 Random 88.06263 TRUE 300 Random 95.8476

TABLE 9D Performance of Uncensored Inference with Affinity Reagentshaving Random Off-Target Sites and Targeting the 300 Optimal Trimers inthe Proteome Number of Censored Cycles Probe Type Sensitivity FALSE 100Random 65.72841 FALSE 200 Random 96.38012 FALSE 300 Random 98.56092

The performance of the optimized probe sets for both censored proteininference and uncensored protein inference are plotted in FIG. 18.

Using the set of affinity reagents selected by the greedy optimizationalgorithm improves the performance of both random and biosimilaraffinity reagent sets using both censored protein inference anduncensored protein inference approaches. Additionally, random affinityreagents sets perform almost identically to biosimilar affinity reagentssets when the greedy approach is used to select affinity reagents.

Example 19: Protein Inference Using Binding of Mixtures of AffinityReagents

The methods described herein may be applied to analyze and/or identifyproteins that have been measured using mixtures of affinity reagents.The probability of a specific protein generating a binding outcome whenassayed by a mixture of affinity reagents may be computed as follows:

1) Calculate p_(ns) , the average probability of non-specific epitopebinding of each affinity reagent in the mixture.

-   -   2) Calculate the number of binding sites on the protein based on        the length of the protein (L) and the length of the affinity        reagent epitopes (K): Num binding sites=L−K+1. The probability        of no non-specific binding events occurring is (1−p_(ns)        )^(L−K+1).    -   3) For each affinity reagent in the mixture, calculate the        probability of no epitope-specific binding events occurring:

${{P\_ no}{\_ spec}{\_ bind}({AR})} = {\prod\limits_{epitope}\left( {1 - {{epitope}\mspace{14mu}{binding}\mspace{14mu}{probability}}} \right)^{{epitope}\mspace{14mu}{count}\mspace{14mu}{in}\mspace{14mu}{protein}}}$

-   -   4) The probability of the mixture generating a non-binding        outcome for the protein is:

${P\left( {{no}\mspace{14mu}{bind}} \middle| {protein} \right)} = {\left( {1 - \overset{\_}{p_{ns}}} \right)^{L - K + 1}{\prod\limits_{AR}{{P\_ no}{\_ spec}{\_ bind}({AR})}}}$

-   -   5) The probability of the mixture generating a binding outcome        is:        P(bind|protein)=1−P(no bind|protein)

This approach for calculating the probability of a binding ornon-binding outcome from a protein mixture was used in combination withthe methods described herein to analyze the performance of mixtures ofaffinity reagents for protein identification. Each individual affinityreagent in the analysis binds to its targeted trimer epitope with aprobability of 0.25 and the 4 most similar trimers to that epitopetarget with a probability of 0.25. For these affinity reagents, trimersimilarity is calculated by summing the coefficients from the BLOSUM62substitution matrix for the amino acids at each sequence location in thetrimers being compared. Additionally, each affinity reagent binds 20additional off-target sites with binding probability scaled depending onthe sequence similarity between the off-target site and the targetedtrimer calculated using the BLOSUM62 substitution matrix. Theprobability for these additional off target sites is: 0.25*1.5^(S) ^(OT)^(−S) ^(self) where S_(OT) is the BLOSUM62 similarity between theoff-target site and the targeted site, and S_(self) is the BLOSUM62similarity between the targeted sequence and itself. Any off-targetsites with binding probability below 2.45×10⁸ are adjusted to havebinding probability 2.45×10⁸. The non-specific epitope bindingprobability is 2.45×10⁸ in this example.

An optimal set of 300 mixtures of affinity reagents were generated forboth censored and uncensored protein inference using a greedy approach:

-   -   1) Initialize an empty list of selected affinity reagent (AR)        mixtures.    -   2) Initialize a list of candidate affinity reagents (in this        example, consisting of the 300 most optimal computed using the        greedy approach detailed in Example 18).    -   3) Select a set of protein sequences to optimize against (e.g.,        all human proteins in the Uniprot reference proteome).    -   4) Repeat the following until the desired number of AR mixtures        has been generated:        -   a. Initialize an empty mixture.        -   b. For each candidate AR:            -   i. Simulate binding outcomes using the current mixture                with the candidate AR added to it.            -   ii. Perform protein inference for each protein using the                simulated binding measurements from i. and simulated                binding measurements from previously generated mixtures.            -   iii. Calculate a score for the mixture with this                candidate AR by summing up the probability of the                correct protein identification for each protein as                determined by protein inference.        -   c. Add the highest scoring candidate AR to the mixture.        -   d. For each candidate AR not already in the mixture, score            the mixture with the addition of the AR, as in i-iii, and if            the highest scoring candidate has a higher score than the            previous candidate added to the mixture, add it to the            mixture and repeat this step. The mixture is complete when            the best scoring candidate AR reduces the score of the            mixture relative to the previously added candidate or when            all candidate ARs have been added to the mixture.

FIG. 19 shows the protein identification sensitivity when the unmixedcandidate affinity reagents are used with censored protein inference anduncensored protein inference, and when mixtures are used. The dataplotted in FIG. 19 is shown in Tables 10A-10B.

Tables 10A-B

TABLE 10A Performance of Censored Inference with Measurements Made onIndividual Probe Binding (unmix) or Mixtures of Probes (mix) Number ofCensored Mix Type Cycles Probe Type Sensitivity TRUE mix 100 Biosimilar2.244199 TRUE unmix 100 Biosimilar 1.363002 TRUE mix 200 Biosimilar72.16939 TRUE unmix 200 Biosimilar 76.51198 TRUE mix 300 Biosimilar86.91518 TRUE unmix 300 Biosimilar 91.5684

TABLE 10B Performance of Uncensored Inference with Measurements Made onIndividual Probe Binding (unmix) or Mixtures of Probes (mix) Number ofCensored Mix Type Cycles Probe Type Sensitivity FALSE mix 100 Biosimilar65.76011 FALSE unmix 100 Biosimilar 50.79244 FALSE mix 200 Biosimilar97.81286 FALSE unmix 200 Biosimilar 96.30404 FALSE mix 300 Biosimilar99.14416 FALSE unmix 300 Biosimilar 98.56726

The use of mixtures improves performance when uncensored inference isused but may negatively impact performance if censored inference isused.

Example 20—Glycan Identification with a Database of 7 Candidate Glycans

Consider a situation where a database contains 7 candidate glycans:

ID Structure 19 Galb1-4GlcNAcb1-6(Galb1-4GlcNAcb1-3)GalNAc 52GlcNAcb1-2Mana1-6(GlcNAcb1-2Mana1-3)Manb1-4GlcNAcb1- 4GlcNAc 344GlcNAca1-4Galb1-3 GalNAc 378 Neu5Aca2-3Galb1-4(Fuca1-3)GlcNAcb1-3GalNAc430 Fuca1-3GlcNAcb1-6(Galb1-4GlcNAcb1-3)Galb1-4Glc 519GalNAca1-3(Fuca1-2)Galb1-4GlcNAcb1-6GalNAc 534Neu5Aca2-3Galb1-4(Fuca1-3)GlcNAcb1-2Man

Additionally, the experiment is performed with 4 affinity reagents (AR),each of which has a 25% likelihood of binding a given disaccharide. Theother disaccharides these reagents bind to are not found in any glycanin the database.

A hit table is constructed for the affinity reagents to each sequence inthe database (Row=affinity reagents #1 to #4, Col=SEQ ID)

AR Target 19 52 344 378 430 519 534 Neu5Aca2-3Gal 1 1 GlcNAcb1-2Man 2 1Fuca1-3GlcNAc 1 1 1 Galb1-4GlcNAc 2 1 1 1 1

Notably, this information arrives incrementally, and therefore may becomputed iteratively. From the hit table, P(glycan_i|AR_j) is evaluatedto generate a probability matrix, as shown below. Note that for a givenentry, if hit table≥1, then use P_landing_AR_n=true landing rate=0.25;else if hit table=0, use P(detector error)=0.00001.

19 52 344 378 430 519 534 Neu5Aca2-3Gal 1.00E−05 1.00E−05 1.00E−05 0.251.00E−05 1.00E−05 0.25 GlcNAcb1-2Man 1.00E−05 0.25 1.00E−05 1.00E−051.00E−05 1.00E−05 0.25 Fuca1-3GlcNAc 1.00E−05 1.00E−05 1.00E−05 0.250.25 1.00E−05 0.25 Galb1-4GlcNAc 0.25 1.00E−05 1.00E−05 0.25 0.25 0.250.25

Note that many of the cells contain a 0.00001 probability. This smallprobability accounts for possible detector error. The initial,un-normalized probability of a glycan is calculated as the product ofthe probabilities for each candidate glycan:

19 52 344 378 430 519 534 2.5E−16 2.5E−16 1E−20 1.5625E−07 6.25E−122.5E−16 0.00390625

Next, the size normalization is computed, which refers to the number ofways some number of affinity reagents may land on a given glycan, as afunction of the number of potential binding sites of the glycan. Thesize normalization is given by the Choose(sites_i, n) term. For example,candidate ID 52 has 6 disaccharide sites and a size normalization of [6choose 4] which is 15. If there are more binding events than the numberof available disaccharide sites, the size normalization factor is setto 1. The un-normalized probabilities of each glycan are normalized totake into account this size correction by dividing by the sizenormalization which gives:

19 52 344 378 430 519 534 2.5E−16 1.6667E−17 1E−20 1.5625E−07 1.25E−122.5E−16 0.00390625

Next, the probabilities are normalized such that the entire set ofprobabilities over the entire database sums up to one. This is achievedby summing the size-normalized probabilities to 0.00390641 and dividingeach of the size-normalized probabilities by this normalization toachieve the final balanced probabilities:

19 52 344 378 430 519 534 6.39974E−14 4.2665E−15 2.5599E−18 3.9998E−053.1999E−10 6.3997E−14 0.99996

Example 21: Performance of Censored Protein Identification in SamplesContaining Protein Isoforms

The protein identification approaches described herein may be applied tosamples containing protein isoforms. An isoform of a canonical proteinmay refer to a variant of the canonical protein formed by alternativesplicing of the same gene as the canonical protein or another gene inthe same gene family as the canonical protein. A protein isoform may bestructurally similar to the canonical protein, typically sharing largeportions of sequence with the canonical protein.

Protein Sample and Affinity Reagents

To determine the impact of the presence of isoform sequences on proteinidentification, an affinity reagent binding analysis was performed on acollection of proteins consisting of 20,374 unique canonical humanproteins and 21,987 unique isoforms of those canonical proteins. Thecanonical proteins and isoform proteins are those listed in thereference human proteome available as part of the Uniprot database. Onlyproteins with the “Swiss-Prot” designation, used to designate proteinsthat have been manually annotated and reviewed, were included in theanalysis. The number of isoforms included for each individual canonicalprotein ranged from 0 to 36 isoforms. The mean number of isoforms for acanonical protein in this set is 1.08. The sample was analyzed using 384affinity reagent cycles, each cycle measuring binding outcomes of aunique affinity reagent to each of the proteins in the sample. Eachaffinity reagent binds a targeted trimer with a probability of 0.25, andto the four trimers most similar to the targeted trimer with aprobability of 0.25. Other off-target trimers are bound with aprobability of the greater of the quantities 2.45×10⁻⁸ and 0.25*1.5^(−x)where x is the similarity of the off-target trimer to the trimer targetsubtracted from the similarity of the targeted trimer to itself. Thesimilarity between trimer sequences can be computed by, for example,summing the BLOSUM62 coefficient for the amino acid pair at each of thethree sequence locations. Affinity reagent trimer targets were selectedusing a greedy approach, as described in Example 18, to optimize againstthe human proteome.

Protein Identification Performance Using Unknown Isoform Sequences

Censored protein inference was performed on the binding outcomes fromthe sample using a database containing only the sequences for the 20,374canonical proteins in the protein sample. Because the database used forprotein inference is missing the sequences of the 21,987 proteinisoforms in the sample, the results of this analysis indicateperformance when the sequences of potential protein isoforms in a sampleare not known. With protein inference performed in this manner, thecorrect protein family is identified for 83.9% of the proteins in thesample with a false discovery rate of 1%. The term “protein family,” asused herein, generally refers to a set of sequences including acanonical protein sequence and all isoforms of that canonical proteinsequence. The correct protein family for a protein is identified if theinferred protein identity is within the same protein family as theprotein being analyzed.

Protein Identification Performance Using Known Isoform Sequences

When protein inference was performed using a sequence databaseconsisting of all of the protein sequences in the sample (both canonicalprotein sequences and isoform protein sequences), the correct proteinsequence was identified for 60.9% of the proteins in the sample with afalse discovery rate of 1%. The correct protein sequence is identifiedfor a protein if the exact sequence for the protein is identified.Further, the correct protein family is identified for 89.8% of theproteins in the sample. The discrepancy between the identification rateof protein families and of exact protein sequences may arise due to thedifficulty of resolving the identity of a protein between multipleisoform candidates having similar sequences.

Protein Identification Performance Using Protein Families Defined aPriori

When the grouping of canonical protein sequences and isoform proteinsequences into protein families is known a priori, the identificationrate for protein families may be improved by calculating protein familyprobabilities directly. For an individual protein being measured, theprobability of the protein being a member of the protein family may becalculated by summing each of the probabilities of the individualprotein sequences comprising the family. The protein family with thehighest probability for the protein being analyzed is assigned as theprotein family identification. When protein family probabilities arecalculated in this manner, the correct protein family is identified for97.2% of the proteins in the sample at 1% false discovery rate. Incomparison, the correct protein family is identified for 89.8% of theproteins in the sample at 1% false discovery rate, when the proteinfamily probabilities are not directly calculated.

Example 22: Performance of Censored Protein Identification in SamplesContaining Proteins with Single Amino Acid Variants (SAVs)

The protein identification approaches described herein may be applied tosamples containing proteins with single amino acid variants. A singleamino acid variant (SAV) of a canonical protein, as used herein,generally refers to a variant of the canonical protein which differs bya single amino acid. Single amino acid variant proteins may typicallyarise from missense single nucleotide polymorphisms (SNPs) in the geneencoding the protein.

Protein Sample and Affinity Reagents

To determine the impact of the presence of SAV proteins on proteinidentification, an affinity reagent binding analysis was performed on acollection of proteins consisting of 20,374 unique canonical humanproteins and 12,827 unique SAVs of those canonical proteins. Thecanonical proteins are those listed in the reference human proteomeavailable as part of the Uniprot database. For each canonical protein,if one or more SAVs for the protein exist in the SAV database, arandomly chosen SAV is included in the sample. The SAV database used isthe Uniprot human polymorphisms and disease mutations index. Onlyproteins with the “Swiss-Prot” designation, used to designate proteinsthat have been manually annotated and reviewed, were included in theanalysis. The sample was analyzed using 384 affinity reagent cycles,each cycle measuring binding outcomes of a unique affinity reagent toeach of the proteins in the sample. Each affinity reagent binds atargeted trimer with a probability of 0.25, and to the four trimers mostsimilar to the targeted trimer with a probability of 0.25. Otheroff-target trimers are bound with a probability of the greater of thequantities 2.45×10⁻⁸ and 0.25*1.5^(−x) where x is the similarity of theoff-target trimer to the trimer target subtracted from the similarity ofthe targeted trimer to itself. The similarity between trimer sequencesmay be computed by, for example, summing the BLOSUM62 coefficient forthe amino acid pair at each of the three sequence locations. Affinityreagent trimer targets were selected using a greedy approach, asdescribed in Example 18, to optimize against the human proteome.

Protein Identification Performance Using Known SAV Sequences

Censored protein inference was performed on the binding outcomes fromthe sample using a database containing only the sequences for the 20,374canonical proteins in the protein sample. Because the database used forprotein inference is missing the sequences of the 12,827 SAV proteins inthe sample, the results of this analysis indicate performance when thesequences of all potential SAVs in a sample are not known. With proteininference performed in this manner, the correct SAV protein family isidentified for 96.0% of the proteins in the sample with a falsediscovery rate of 1%. The term “SAV protein family,” as used herein,generally refers to set of sequences including a canonical proteinsequence and all SAVs of that canonical protein sequence. The correctSAV protein family for a protein is identified if the inferred proteinidentity is within the same SAV protein family as the protein beinganalyzed.

Protein Identification Performance Using Known SAV Sequences

When protein inference was performed using a sequence databaseconsisting of all of the protein sequences in the sample (both canonicalprotein sequences and SAV protein sequences), the correct proteinsequence was identified for 27.1% of the proteins in the sample with afalse discovery rate of 1%. The correct protein sequence is identifiedfor a protein if the exact sequence for the protein is identified.Further, the correct SAV protein family is identified for 96.1% of theproteins in the sample. The discrepancy between the identification rateof SAV protein families and of exact protein sequences may arise due tothe difficulty of resolving between the identities of a canonicalprotein sequence and of an extremely similar SAV sequence.

Protein Identification Performance Using SAV Protein Families Defined aPriori

The identification rate for SAV protein families may be improved bycalculating SAV protein family probabilities directly. For an individualprotein being measured, the probability of the protein being a member ofa SAV protein family may be calculated by summing each of theprobabilities of the individual protein sequences comprising the family.The SAV protein family with the highest probability for the proteinbeing analyzed is assigned as the SAV protein family identification.When SAV protein family probabilities are calculated in this manner, thecorrect SAV protein family is identified for 96.5% of the proteins inthe sample at 1% false discovery rate. In comparison, the correct SAVprotein family is identified for 96.1% of the proteins in the sample at1% false discovery rate when the protein family probabilities are notdirectly calculated.

Example 23: Performance of Censored Protein Inference on a SampleContaining Proteins from a Mixture of Species

In some cases, a protein sample may comprise proteins from each of aplurality of species. A protein sample may contain proteins arising fromexternal sources such as fossils. In some embodiments, a protein samplemay contain proteins that are synthesized, modified, or engineered, suchas a recombinant protein, or a protein synthesized by in-vitrotranscription and translation. In some embodiments, synthesized,modified, or engineered proteins may contain non-natural sequences(e.g., arising from CRISPR-Cas9 modification or other artificial geneconstructs). Each of the species may be, for example, an animal such asa mammal (e.g., human, mouse, rat, primate, or simian), farm animals(production cattle, dairy cattle, poultry, horses, pigs, and the like),sport animals, companion animals (e.g., pet or support animals); aplant, a protist, a bacterium, a virus, or an archeon.

In this example, a sample from a mouse tumor xenograft model maycomprise substantial amounts of proteins of both mouse and human origin.To determine the performance of protein inference on a sample havingproteins from a mixture of species on protein inference, an affinityreagent binding analysis was performed on a collection of proteinsconsisting of 2,000 unique mouse proteins and 2,000 unique humanproteins. Both the human proteins and the mouse proteins were randomlyselected from the collection of canonical Swiss-Prot sequence entries inthe Uniprot reference proteome of the respective species. The sample wasanalyzed using 384 affinity reagent cycles, each cycle measuring bindingoutcomes of a unique affinity reagent to each of the proteins in thesample. Each affinity reagent binds a targeted trimer with a probabilityof 0.25, and to the four trimers most similar to the targeted trimerwith a probability of 0.25. Other off-target trimers are bound withprobability the greater of the quantities 2.45×10⁻⁸ and 0.25*1.5^(−x)where x is the similarity of the off-target trimer to the trimer targetsubtracted from the similarity of the targeted trimer to itself. Thesimilarity between trimer sequences may be computed by, for example,summing the BLOSUM62 coefficient for the amino acid pair at each of thethree sequence locations. Affinity reagent trimer targets were selectedusing a greedy approach, as described in Example 18, to optimize againstthe human proteome.

When protein inference was performed on the mixture sample using adatabase containing only the sequences for the candidate proteins fromthe human proteome (canonical Swiss-Prot sequence entries in the Uniprothuman reference proteome), the results showed no identifications ofproteins in the sample (e.g., an identification rate of 0%) below a 1%false discovery rate threshold. In comparison, when protein inferencewas performed on the mixture sample using a database containing thesequences for the candidate proteins from both the human proteome andthe mouse proteome, 85.3% of the proteins in the sample were identifiedbelow a 1% false discovery rate threshold. This discrepancy inperformance indicates that for a sample containing proteins frommultiple species (e.g., a mixture sample), protein identificationperformance is significantly improved when protein inference analysis isperformed using a database containing the sequences for the candidateproteins from all of the species represented in the mixture sample.

Example 24: Design of an Affinity Reagent Set Against a Targeted Panelof Proteins

A set of affinity reagents may be designed that is optimized foridentification of a specific subset of proteins in a sample. Forexample, an optimal collection of affinity reagents can be used toidentify a specific set of target proteins in fewer affinity reagentbinding cycles as compared to using a set optimized for identificationof the entire proteome. In this example, a set of affinity reagents isgenerated for optimal identification of 25 human proteins, which arepotential biomarkers for clinical response to cancer immunotherapytreatment. The proteins in the targeted panel are listed in Table 11.

TABLE 11 Proteins Included in the Targeted Panel for Response to CancerImmunotherapy Uniprot Category Gene Accessions T cell surface CD8AP01732 markers CD3 P07766; P09693; P20963; P04234 CD2 P06729 CD38 P28907Cytotoxic factors PRF1 P14222 GZMB P10144 Tissue rejection- CXCL9 Q07325related CXCL10 P02778 cytokines and CXCL2 P19875 chemokines CXCL11O14625 CCL4 P13236 CCL5 P13501 GZMK P49863 PD-1/immune PD-L1 Q9NZQ7checkpoints JAK2 O60674 PD-L2 Q9BQ51 PD-1 Q15116 CTLA4 P16410 Increasedtype 1 IFNG P01579 immunity & cytotoxic cell activity Interleukins IL-12P29459; P29460 IL-2 P60568

To generate a set of affinity reagents optimized for identification ofthe complete proteome, a greedy selection approach, as described inExample 18, was applied. This set of affinity reagents can be referredto as the “proteome-optimized” affinity reagent set. To generate a setof affinity reagents optimized for identification of the proteins inTable 11, a modified version of step 4) i) in Example 18 is performed,in which, rather than calculating the score for the candidate affinityreagent by summing each of the probabilities of the correct proteinidentification for each protein determined by protein inference, thescore for the candidate affinity reagent is calculated by summing eachof the probabilities of the correct protein identification for only theproteins in the targeted panel. This affinity reagent set can bereferred to as the “panel-optimized” affinity reagent set. Theperformance of the proteome-optimized and panel-optimized affinityreagent sets were tested on a human proteome sample containing everyunique, canonical protein in the Swiss-Prot human reference proteomefrom Uniprot (20,374 proteins). This sample includes all 25 of theproteins in the target panel. Both affinity reagents sets were used toanalyze the protein sample, and censored inference used to generateprotein identifications for every protein in the sample.

The number of targeted panel proteins identified by theproteome-optimized and panel-optimized affinity reagent sets isindicated in Table 12. For a targeted panel protein to be counted as asuccessful identification, it must be present in the list of allproteins identified in the sample at a false discovery rate below 1%.Identification was performed with varying number of affinity reagentcycles. For example, 150 affinity reagent cycles indicates that proteininference was performed on a dataset comprising analysis with the first150 affinity reagents from either the proteome-optimized orpanel-optimized set, with each affinity reagent analyzed in anindividual cycle.

TABLE 12 Protein Identification Performance for Target Panel of 25Target Proteins Target Panel Proteins Target Panel Proteins Number ofAffinity Identified (Proteome- Identified (Panel- Reagent CyclesOptimized Reagents) Optimized Reagents) 50 0 0 100 1 3 150 10 9 200 1819 250 19 24 300 20 24 350 22 24 384 23 24

The results shown in Table 12 indicate that application of thepanel-optimized affinity reagents successfully increased theidentification rate of the targeted panel proteins. The percentage ofall proteins identified at a false discovery rate below 1% for both thepanel-optimized and proteome-optimized affinity reagent sets areindicated in Table 13.

TABLE 13 Protein Identification Performance for All Proteins in theSample % of Proteins Identified % of Proteins Identified in Sample inSample Number of Affinity (Proteome-Optimized (Panel-Optimized ReagentCycles Reagents) Reagents) 50 0 0 100 3.1 0.1 150 43.4 4.7 200 78.9 34.4250 89.2 65.6 300 93.0 77.5 350 94.8 84.2 384 95.7 87.0

The results shown in Table 13 indicate that a panel-optimized affinityreagent set can be generated to improve the performance of identifying aset of proteins in a specific targeted panel. However, a tradeoff may beencountered, wherein the resulting panel-optimized affinity reagent setmay be sub-optimal for identifying proteins outside of the targetedpanel, as indicated by the decreased overall protein identification rateof the panel-optimized reagents in Table 13.

Example 25: Performance of Protein Inference Using Detection ofPresence, Count, or Order of Individual Amino Acids

The protein inference approach described herein may be applied tomeasurements of specific amino acids in proteins and peptides. Forexample, measurements on a protein may be made which indicate thepresence or absence of an amino acid in a protein or peptide (binary),the count of an amino acid in a protein or peptide (count), or the orderof amino acids in a protein (order). In this example, proteins aremodified by a series of reactions which each selectively modify aparticular amino acid. Each reaction of the series of reactions has areaction efficiency between 0 and 1, indicating the probability of thereaction successfully modifying any single amino acid substrate withinthe protein. After performing such modification reactions on the proteinsample, the presence or absence of a selectively-modified amino acid maybe detected, the count of a selectively-modified amino acid may bedetected, and/or the order of a particular set of selectively-modifiedamino acids within the protein may be detected.

Detections from Presence and Absence Measurements of Amino Acids

To generate protein identifications from a sequence of binarymeasurements indicating presence or absence of amino acids, theprobability Pr(amino acid detected present|protein) can be expressed as1−(1−R_(aa))^(Caa) where R_(aa) is the reaction efficiency for the aminoacid and Caa is the count of the number of times the amino acid occursin the protein. The probability Pr(amino acid not detectedpresent|protein) can be expressed as 1−Pr(amino acid detectedpresent|protein). If a sequence of multiple amino acid detectionmeasurements is made, the probabilities may be multiplied to determinethe probability of the complete set of N measurements given a candidateprotein, as expressed by:Pr(outcome set protein)=Pr(measurement outcome for amino acid1|protein)*Pr(measurement outcome for amino acid2|protein)*Pr(measurement outcome for amino acid N|protein).

The probability of a particular candidate protein being the correctidentification for the protein being measured can be expressed as

$\frac{\Pr\left( {{outcome}\mspace{14mu}{set}} \middle| {{candidate}\mspace{14mu}{protein}} \right)}{\sum\limits_{i = 1}^{P}{\Pr\left( {{outcome}\mspace{14mu}{set}} \middle| {protein}_{t} \right)}}$where Σ_(i=1) ^(P) Pr(outcome set|protein_(i)) is the sum of theprobabilities of the outcome set for each possible protein in theprotein sequence database consisting of P proteins.Detections from Count Measurements of Amino Acids

To generate protein identifications from a sequence of countmeasurements of amino acids, the probability Pr(amino acid countmeasurement|protein) can be expressed as

$\left( R_{aa} \right)^{M}*\left( {1 - R_{aa}} \right)^{{C{aa}} - M}*\begin{pmatrix}{Caa} \\M\end{pmatrix}$where R_(aa) is the reaction efficiency for the amino acid, Caa is thecount of the number of times the amino acid occurs in the protein, and Mis the measured count for the amino acid in the protein. If M>Caa, aprobability of 0 is returned. If a sequence of multiple amino acid countmeasurements is made, the probabilities may be multiplied to determinethe probability of the complete set of N measurements given a candidateprotein, as expressed by:Pr(outcome set|protein)=Pr(measurement outcome for amino acid1|protein)*Pr(measurement outcome for amino acid2|protein)*Pr(measurement outcome for amino acid N|protein).

The probability of a particular candidate protein being the correctidentification for the protein being measured can be expressed as

$\frac{\Pr\left( {{outcome}\mspace{14mu}{set}} \middle| {{candidate}\mspace{14mu}{protein}} \right)}{\sum\limits_{i = 1}^{P}{\Pr\left( {{outcome}\mspace{14mu}{set}} \middle| {protein}_{t} \right)}}$where Σ_(i=1) ^(P) Pr(outcome set|protein_(i)) is the sum of theprobabilities of the outcome set for each possible protein in theprotein sequence database consisting of P proteins.Detections from Order Measurements of Amino Acids

In some embodiments, an order of selectively-modified amino acids in aprotein may be measured. For example, a protein with sequence TINYPRTEINmay generate a measurement outcome ININ if amino acids I and N aremodified and measured. Similarly, the same protein may generate ameasurement outcome INN, or IIN, in cases where a subset of amino acidmodifications and/or measurements is not successful. The probabilityPr(measurement outcome|protein) can be expressed asPr(aa_counts|protein)*NUMORDER. The Pr(aa_counts|protein)=Π_(i=1)^(i=L)(R_(aai))^(Mi)*(1−R_(aai))^(Caai−Mi) where R_(aai) is the reactionefficiency for amino acid i, M_(i) is the number of times the amino acidi was measured (e.g., in a measurement outcome of INN, N was measured 2times), C_(aai) is the number of times amino acid i occurs in thesequence of the candidate protein, and amino acids 1 to L are all uniqueamino acids measured in the protein (e.g., I and N, for measurementoutcome ININ). If the number of counts measured for any particular aminoacid is greater than the number of times that amino acid occurs in theprotein candidate sequence, then the probability Pr(aa_counts|protein)is set to zero. NUMORDER is the number of ways a particular outcome canbe generated from the protein sequence. For example, the measurementoutcome of IN can be generated from the protein TINYPRTEIN in thefollowing ways: {TINYPRTEIN, TINYPRTEIN, TINYPRTEIN}, so NUMORDER is 3for this particular outcome and protein sequence. Note that NUMORDER hasa value of zero in cases where it is not possible to generate aparticular outcome from a protein (for example, the measurement outcomeof INNI cannot be generated from the protein TINYPRTEIN). Theprobability of a particular candidate protein being the correctidentification for the protein being measured can be expressed as

$\frac{\Pr\left( {{measurement}\mspace{14mu}{outcome}} \middle| {{candidate}\mspace{14mu}{protein}} \right)}{\sum\limits_{i = 1}^{P}{\Pr\left( {{measurement}\mspace{14mu}{outcome}} \middle| {protein}_{i} \right)}}$where Σ_(i=1) ^(P) Pr(measurement outcome|protein_(i)) is the sum of theprobabilities of the measurement outcome for each possible protein inthe protein sequence database consisting of P proteins. In cases whereΣ_(i=1) ^(P) Pr(measurement outcome|protein_(i)) is equal to zero, theprobability of the candidate protein is set to zero.

The performance of protein identification using a collection of reagentsfor selective modification and detection of amino acids K, D, C, and Wis illustrated in FIG. 22 and Table 14. The reactions are performed withvarying efficiency, as indicated on the x-axis. The detection modality(either “binary,” “count,” or “order,” indicating detection of presenceor absence of amino acids, counts of amino acids, or order of aminoacids, respectively) is indicated by the shade of each bar. The heightof each bar indicates the percent of proteins in the sample identifiedwith a false discovery rate below 1%. The sample measured was a humanprotein sample containing 1,000 proteins. The results indicate that asubstantial number of proteins can be identified using measurements oforder of amino acids with a reaction efficiency of 0.9 or higher. Ifmeasurements of counts of amino acids are used, a substantial number ofproteins can be identified with a reaction efficiency of 0.99 or higher.In none of the tested scenarios was measurement of presence or absenceof amino acids sufficient to generate protein detections.

TABLE 14 Protein Identification Performance using Selective Modificationand Detection of 4 Amino Acids (K, D, C, and W) Experiment ReactionExperiment Name Type Sensitivity Efficiency KDWC Binary 0.5 binary 0 0.5KDWC Count 0.5 count 1 0.5 KDWC Order 0.5 order 58.1 0.5 KDWC Binary 0.9binary 0 0.9 KDWC Count 0.9 count 10.1 0.9 KDWC Order 0.9 order 94.9 0.9KDWC Binary 0.99 binary 0 0.99 KDWC Count 0.99 count 76.4 0.99 KDWCOrder 0.99 order 95.4 0.99 KDWC Binary 0.999 binary 0 0.999 KDWC Count0.999 count 92.2 0.999 KDWC Order 0.999 order 95.2 0.999

As shown in FIG. 23, the collection of reagents for selectivemodification and detection of amino acids was expanded to include the 20amino acids R, H, K, D, E, S, T, N, Q, C, G, P, A, V, I, L, M, F, Y, andW. The detection modality is indicated by the line shade, and thereaction efficiency is indicated on the x-axis. The y-axis indicates thepercent of proteins identified with a false discovery rate below 1% inthe sample.

The results shown in FIG. 23 and Table 15 indicate that such acollection of reagents is very effective at protein identification ifreaction efficiency is greater than about 0.6 and measurements of countsof amino acids are used. However, only a small percentage of proteins isever identified if measurements of presence or absence of amino acidsare used instead of measurements of counts of amino acids.

TABLE 15 Protein Identification Performance using Selective Modificationand Detection of 20 Amino Acids (R, H, K, D, E, S, T, N, Q, C, G, P, A,V, I, L, M, F, Y, and W) Experiment Reaction Experiment Name TypeSensitivity Efficiency All Res Binary 0.1 binary 0 0.1 All Res Count 0.1count 3.2 0.1 All Res Binary 0.2 binary 0.1 0.2 All Res Count 0.2 count7.3 0.2 All Res Binary 0.3 binary 0.5 0.3 All Res Count 0.3 count 21.10.3 All Res Binary 0.4 binary 0.4 0.4 All Res Count 0.4 count 44.7 0.4All Res Binary 0.5 binary 0.8 0.5 All Res Count 0.5 count 74.6 0.5 AllRes Binary 0.6 binary 1.2 0.6 All Res Count 0.6 count 92.4 0.6 All ResBinary 0.7 binary 1.7 0.7 All Res Count 0.7 count 97.1 0.7 All ResBinary 0.8 binary 1.9 0.8 All Res Count 0.8 count 98.6 0.8 All ResBinary 0.9 binary 2.5 0.9 All Res Count 0.9 count 99.9 0.9

FIG. 24 illustrates the performance of protein identification usingmeasurements of order of amino acids, where amino acids are measuredwith a detection probability (equal to reaction efficiency) indicated onthe x-axis. The y-axis indicates the percent of proteins in the sampleidentified with a false discovery rate below 1%. The experiment wasperformed with measurements of order of amino acids measured at theN-terminal 25, 50, 100, or 200 amino acids of each protein, and thecandidate protein sequence database consisted of the first 25, 50, 100,or 200 amino acids, respectively, of each canonical protein sequence inthe Uniprot reference human protein database.

The performance illustrated in FIG. 24 and Table 16 indicates that, withdetection probability of about 0.3, it is optimal to sequence at leastthe first 100 amino acids of each protein. Above a detection probabilityof about 0.6, sequencing the first 25 amino acids or more appears to besufficient.

TABLE 16 Protein Identification Performance using Measurements of Orderof Amino Acids Experiment Detection Sequencing Experiment Name TypeSensitivity Probability Length Sample Order N term 25 order 0.2 0.1N-terminal 25 (Prob 0.1) Sample Order N term 50 order 0.5 0.1 N-terminal50 (Prob 0.1) Sample Order N term 100 order 5.8 0.1 N-terminal 100 (Prob0.1) Sample Order N term 200 order 26 0.1 N-terminal 200 (Prob 0.1)Sample Order N term 25 order 36.2 0.3 N-terminal 25 (Prob 0.3) SampleOrder N term 50 order 82.1 0.3 N-terminal 50 (Prob 0.3) Sample Order Nterm 100 order 96.8 0.3 N-terminal 100 (Prob 0.3) Sample Order N term200 order 97.1 0.3 N-terminal 200 (Prob 0.3) Sample Order N term 25order 70.5 0.4 N-terminal 25 (Prob 0.4) Sample Order N term 50 order96.1 0.4 N-terminal 50 (Prob 0.4) Sample Order N term 100 order 95.8 0.4N-terminal 100 (Prob 0.4) Sample Order N term 200 order 100 0.4N-terminal 200 (Prob 0.4) Sample Order N term 25 order 85.4 0.5N-terminal 25 (Prob 0.5) Sample Order N term 50 order 97.1 0.5N-terminal 50 (Prob 0.5) Sample Order N term 100 order 97.2 0.5N-terminal 100 (Prob 0.5) Sample Order N term 200 order 99.7 0.5N-terminal 200 (Prob 0.5) Sample Order N term 25 order 94.1 0.6N-terminal 25 (Prob 0.6) Sample Order N term 50 order 96.5 0.6N-terminal 50 (Prob 0.6) Sample Order N term 100 order 99 0.6 N-terminal100 (Prob 0.6) Sample Order N term 200 order 100 0.6 N-terminal 200(Prob 0.6) Sample Order N term 25 order 94.3 0.7 N-terminal 25 (Prob0.7) Sample Order N term 50 order 96.6 0.7 N-terminal 50 (Prob 0.7)Sample Order N term 100 order 97.5 0.7 N-terminal 100 (Prob 0.7) SampleOrder N term 200 order 100 0.7 N-terminal 200 (Prob 0.7)

FIG. 25 illustrates the performance of various approaches on a trypticdigest of a sample consisting of 1,000 unique human proteins. The samplecontains all fully tryptic peptides of length greater than 12 with nomissed cleavages arising from these proteins. The dark lines indicateperformance when protein identification is performed using measurementsof the order of all amino acids, which are measured at varying detectionprobability (equivalent to reaction efficiency). The light linesindicate performance when only the order of amino acids K, D, W, and Care measured at varying detection probability (equivalent to reactionefficiency). The sequence database used for inference contains thesequences of every fully tryptic peptide with length greater than 12with no missed cleavages arising from these proteins, derived from everycanonical protein sequence in the human reference proteome databasedownloaded from Uniprot. The solid lines indicate the percentage ofpeptides in the sample identified at a false discovery rate below 1%.The dashed lines indicate the percentage of proteins in the sampleidentified at a false discovery rate below 1%. A protein is identifiedif a peptide with sequence unique to that protein is identified at afalse discovery rate below 1%. These results indicate that measuring theorder of just amino acids K, D, W, and C may not be sufficient forprotein detection from a tryptic digest sample. Further, measuring theorder of all amino acids with a detection probability (equivalent toreaction efficiency) at or above about 0.5 is sufficient to identify themajority of proteins in a tryptic digest.

Computer Control Systems

The present disclosure provides computer control systems that areprogrammed to implement methods of the disclosure. FIG. 10 shows acomputer system 1001 that is programmed or otherwise configured to:receive information of empirical measurements of unknown proteins in asample, compare information of empirical measurements against a databasecomprising a plurality of protein sequences corresponding to candidateproteins, generate probabilities of a candidate protein generating theobserved measurement outcome set, and/or generate probabilities thatcandidate proteins are correctly identified in the sample.

The computer system 1001 can regulate various aspects of methods andsystems of the present disclosure, such as, for example, receivinginformation of empirical measurements of unknown proteins in a sample,comparing information of empirical measurements against a databasecomprising a plurality of protein sequences corresponding to candidateproteins, generating probabilities of a candidate protein generating theobserved measurement outcome set, and/or generating probabilities thatcandidate proteins are correctly identified in the sample.

The computer system 1001 can be an electronic device of a user or acomputer system that is remotely located with respect to the electronicdevice. The electronic device can be a mobile electronic device. Thecomputer system 1001 includes a central processing unit (CPU, also“processor” and “computer processor” herein) 1005, which can be a singlecore or multi core processor, or a plurality of processors for parallelprocessing. The computer system 1001 also includes memory or memorylocation 1010 (e.g., random-access memory, read-only memory, flashmemory), electronic storage unit 1015 (e.g., hard disk), communicationinterface 1020 (e.g., network adapter) for communicating with one ormore other systems, and peripheral devices 1025, such as cache, othermemory, data storage and/or electronic display adapters. The memory1010, storage unit 1015, interface 1020 and peripheral devices 1025 arein communication with the CPU 1005 through a communication bus (solidlines), such as a motherboard. The storage unit 1015 can be a datastorage unit (or data repository) for storing data. The computer system1001 can be operatively coupled to a computer network (“network”) 1030with the aid of the communication interface 1020. The network 1030 canbe the Internet, an internet and/or extranet, or an intranet and/orextranet that is in communication with the Internet. The network 1030 insome cases is a telecommunication and/or data network. The network 1030can include one or more computer servers, which can enable distributedcomputing, such as cloud computing. For example, one or more computerservers may enable cloud computing over the network 1030 (“the cloud”)to perform various aspects of analysis, calculation, and generation ofthe present disclosure, such as, for example, receiving information ofempirical measurements of unknown proteins in a sample, comparinginformation of empirical measurements against a database comprising aplurality of protein sequences corresponding to candidate proteins,generating probabilities of a candidate protein generating the observedmeasurement outcome set, and/or generating probabilities that candidateproteins are correctly identified in the sample. Such cloud computingmay be provided by cloud computing platforms such as, for example,Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform, andIBM cloud. The network 1030, in some cases with the aid of the computersystem 1001, can implement a peer-to-peer network, which may enabledevices coupled to the computer system 1001 to behave as a client or aserver.

The CPU 1005 can execute a sequence of machine-readable instructions,which can be embodied in a program or software. The instructions may bestored in a memory location, such as the memory 1010. The instructionscan be directed to the CPU 1005, which can subsequently program orotherwise configure the CPU 1005 to implement methods of the presentdisclosure. Examples of operations performed by the CPU 1005 can includefetch, decode, execute, and writeback.

The CPU 1005 can be part of a circuit, such as an integrated circuit.One or more other components of the system 1001 can be included in thecircuit. In some cases, the circuit is an application specificintegrated circuit (ASIC).

The storage unit 1015 can store files, such as drivers, libraries andsaved programs. The storage unit 1015 can store user data, e.g., userpreferences and user programs. The computer system 1001 in some casescan include one or more additional data storage units that are externalto the computer system 1001, such as located on a remote server that isin communication with the computer system 1001 through an intranet orthe Internet.

The computer system 1001 can communicate with one or more remotecomputer systems through the network 1030. For instance, the computersystem 1001 can communicate with a remote computer system of a user.Examples of remote computer systems include personal computers (e.g.,portable PC), slate or tablet PC's (e.g., Apple® iPad, Samsung® GalaxyTab), telephones, Smart phones (e.g., Apple® iPhone, Android-enableddevice, Blackberry®), or personal digital assistants. The user canaccess the computer system 1001 via the network 1030.

Methods as described herein can be implemented by way of machine (e.g.,computer processor) executable code stored on an electronic storagelocation of the computer system 1001, such as, for example, on thememory 1010 or electronic storage unit 1015. The machine executable ormachine readable code can be provided in the form of software. Duringuse, the code can be executed by the processor 1005. In some cases, thecode can be retrieved from the storage unit 1015 and stored on thememory 1010 for ready access by the processor 1005. In some situations,the electronic storage unit 1015 can be precluded, andmachine-executable instructions are stored on memory 1010.

The code can be pre-compiled and configured for use with a machinehaving a processer adapted to execute the code, or can be compiledduring runtime. The code can be supplied in a programming language thatcan be selected to enable the code to execute in a pre-compiled oras-compiled fashion.

Aspects of the systems and methods provided herein, such as the computersystem 1001, can be embodied in programming. Various aspects of thetechnology may be thought of as “products” or “articles of manufacture”typically in the form of machine (or processor) executable code and/orassociated data that is carried on or embodied in a type of machinereadable medium. Machine-executable code can be stored on an electronicstorage unit, such as memory (e.g., read-only memory, random-accessmemory, flash memory) or a hard disk. “Storage” type media can includeany or all of the tangible memory of the computers, processors or thelike, or associated modules thereof, such as various semiconductormemories, tape drives, disk drives and the like, which may providenon-transitory storage at any time for the software programming. All orportions of the software may at times be communicated through theInternet or various other telecommunication networks. Suchcommunications, for example, may enable loading of the software from onecomputer or processor into another, for example, from a managementserver or host computer into the computer platform of an applicationserver. Thus, another type of media that may bear the software elementsincludes optical, electrical and electromagnetic waves, such as usedacross physical interfaces between local devices, through wired andoptical landline networks and over various air-links. The physicalelements that carry such waves, such as wired or wireless links, opticallinks or the like, also may be considered as media bearing the software.As used herein, unless restricted to non-transitory, tangible “storage”media, terms such as computer or machine “readable medium” refer to anymedium that participates in providing instructions to a processor forexecution.

Hence, a machine readable medium, such as computer-executable code, maytake many forms, including but not limited to, a tangible storagemedium, a carrier wave medium or physical transmission medium.Non-volatile storage media include, for example, optical or magneticdisks, such as any of the storage devices in any computer(s) or thelike, such as may be used to implement the databases, etc. shown in thedrawings. Volatile storage media include dynamic memory, such as mainmemory of such a computer platform. Tangible transmission media includecoaxial cables; copper wire and fiber optics, including the wires thatcomprise a bus within a computer system. Carrier-wave transmission mediamay take the form of electric or electromagnetic signals, or acoustic orlight waves such as those generated during radio frequency (RF) andinfrared (IR) data communications. Common forms of computer-readablemedia therefore include for example: a floppy disk, a flexible disk,hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD orDVD-ROM, any other optical medium, punch cards paper tape, any otherphysical storage medium with patterns of holes, a RAM, a ROM, a PROM andEPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wavetransporting data or instructions, cables or links transporting such acarrier wave, or any other medium from which a computer may readprogramming code and/or data. Many of these forms of computer readablemedia may be involved in carrying one or more sequences of one or moreinstructions to a processor for execution.

The computer system 1001 can include or be in communication with anelectronic display 1035 that comprises a user interface (UI) 1040 forproviding, for example, user selection of algorithms, bindingmeasurement data, candidate proteins, and databases. Examples of UIsinclude, without limitation, a graphical user interface (GUI) andweb-based user interface.

Methods and systems of the present disclosure can be implemented by wayof one or more algorithms. An algorithm can be implemented by way ofsoftware upon execution by the central processing unit 1005. Thealgorithm can, for example, receive information of empiricalmeasurements of unknown proteins in a sample, compare information ofempirical measurements against a database comprising a plurality ofprotein sequences corresponding to candidate proteins, generateprobabilities of a candidate protein generating the observed measurementoutcome set, and/or generate probabilities that candidate proteins arecorrectly identified in the sample.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. It is not intendedthat the invention be limited by the specific examples provided withinthe specification. While the invention has been described with referenceto the aforementioned specification, the descriptions and illustrationsof the embodiments herein are not meant to be construed in a limitingsense. Numerous variations, changes, and substitutions will now occur tothose skilled in the art without departing from the invention.Furthermore, it shall be understood that all aspects of the inventionare not limited to the specific depictions, configurations or relativeproportions set forth herein which depend upon a variety of conditionsand variables. It should be understood that various alternatives to theembodiments of the invention described herein may be employed inpracticing the invention. It is therefore contemplated that theinvention shall also cover any such alternatives, modifications,variations or equivalents. It is intended that the following claimsdefine the scope of the invention and that methods and structures withinthe scope of these claims and their equivalents be covered thereby.

What is claimed is:
 1. A protein characterization system, comprising:(a) a solid support comprising a plurality of attached proteins, whereinindividual attached proteins of the plurality of attached proteins areoptically resolvable from each other; (b) a set of different affinityreagents configured to bind with at least one of the plurality ofattached proteins, wherein individual affinity reagents in the set ofdifferent affinity reagents recognize target epitopes present inmultiple different proteins of the plurality of attached proteins; (c) adetector configured to measure empirical measurement outcomes forindividual attached proteins of the plurality of attached proteins; (d)a database comprising a set of candidate proteins; and (e) a computerprocessor programmed to (i) receive empirical measurement outcomesmeasured by the detector, (ii) receive candidate proteins from thedatabase, (iii) determine a non-zero probability of affinity reagents ofthe set of different affinity reagents binding to off-target epitopes inthe candidate proteins received by the computer processor, and (iv)output a most probable identity, selected from the candidate proteinsreceived by the computer processor, for an attached protein of theplurality of attached proteins given the empirical measurement outcomesreceived by the computer processor.
 2. The system of claim 1, whereinthe empirical measurement outcomes comprise binding of an individualprotein of the plurality of attached proteins with an affinity reagentof the set of different affinity reagents.
 3. The system of claim 2,wherein the empirical measurement outcomes further comprise non-bindingof an individual protein of the plurality of attached proteins with theaffinity reagent of the set of different affinity reagents.
 4. Thesystem of claim 1, wherein the database further comprises parameters fordetermining a probability of the set of different affinity reagentsgenerating the empirical measurement outcomes for the set of candidateproteins.
 5. The system of claim 1, wherein the computer system isfurther configured to determine a probability that a measurement outcomeset is observed given a hypothesized identity, selected from the set ofcandidate proteins, for an attached protein of the plurality of attachedproteins.
 6. The system of claim 5, wherein the measurement outcome setcomprises a plurality of independent measurement empirical outcomesgenerated by the detector.
 7. The system of claim 1, wherein thecomputer system is further configured to determine a probability orlikelihood that each of the candidate proteins received by the computerprocessor would generate each of the empirical measurement outcomesreceived by the computer processor.
 8. The system of claim 7, whereinthe computer system is further configured to determine a probability ofthe most probable identity being correct given that a measurementoutcome set is observed.
 9. The system of claim 8, wherein themeasurement outcome set comprises a plurality of independent empiricalmeasurement outcomes generated by the detector.
 10. The system of claim1, wherein the computer system is further configured to determine aprobability or a likelihood that a candidate protein from the databasewould generate the empirical measurement outcomes for the individualattached proteins of the plurality of attached proteins.
 11. The systemof claim 1, wherein the computer system is further configured todetermine a probability or a likelihood that a candidate protein fromthe database would not generate the empirical measurement outcomes forthe individual attached proteins of the plurality of attached proteins.12. The system of claim 1, wherein the computer system is furtherconfigured to determine a probability or a likelihood that the empiricalmeasurement outcomes are not observed for a candidate protein from thedatabase.
 13. The system of claim 1, wherein the plurality of attachedproteins comprises at least 500 different proteins.
 14. The system ofclaim 1, wherein the computer system is further configured to quantify anumber of identifications generated for a unique candidate protein ofthe set of candidate proteins to determine the quantity of the uniquecandidate protein in a protein sample.
 15. The system of claim 14,wherein the protein sample is obtained or derived from a subject. 16.The system of claim 1, wherein the detector is further configured tomeasure the binding of the set of different affinity reagents with theplurality of attached proteins with a false detection rate of less than1%.
 17. The system of claim 1, wherein the detector is furtherconfigured to measure the binding of the set of different affinityreagents with the plurality of attached proteins using fluorescencedetection.
 18. The system of claim 1, wherein the database comprisesprotein sequences of the set of candidate proteins.
 19. The system ofclaim 1, wherein the set of candidate proteins comprises a humanreference proteome.
 20. The system of claim 1, wherein the plurality ofattached proteins comprises proteins isolated from a biological sample.21. The system of claim 20, wherein the biological sample is obtainedfrom a subject suspected of having a disease or disorder.
 22. The systemof claim 20, wherein the plurality of attached proteins comprisespost-translational modifications from the biological sample.